Vertebrate smoothened antibodies

ABSTRACT

Novel vertebrate homologues of Smoothened, including human and rat Smoothened, are provided. Compositions including vertebrate Smoothened chimeras, nucleic acid encoding vertebrate Smoothened, and antibodies to vertebrate Smoothened, are also provided.

This is a divisional of application Ser. No. 08/720,484 filed on Sep.30, 1996, U.S. Pat. No. 5,990,281, which application is incorporatedherein by reference and to which application priority is claimed under35 USC §120.

FIELD OF THE INVENTION

The present invention relates generally to novel Smoothened proteinswhich interact with Hedgehog and Patched signalling molecules involvedin cell proliferation and differentiation. In particular, the inventionrelates to newly identified and isolated vertebrate Smoothened proteinsand DNA encoding the same, including rat and human Smoothened, and tovarious modified forms of these proteins, to vertebrate Smoothenedantibodies, and to various uses thereof.

BACKGROUND OF THE INVENTION

Development of multicellular organisms depends, at least in part, onmechanisms which specify, direct or maintain positional information topattern cells, tissues, or organs. Various secreted signallingmolecules, such as members of the transforming growth factor-beta(“TGF-beta”), Wnt, fibroblast growth factor (“FGF”), and hedgehogfamilies, have been associated with patterning activity of differentcells and structures in Drosophila as well as in vertebrates [Perrimon,Cell, 80:517-520 (1995)].

Studies of Drosophila embryos have revealed that, at cellular blastodermand later stages of development, information is maintained across cellborders by signal transduction pathways. Such pathways are believed tobe initiated by extracellular signals like Wingless (“Wg”) and Hedgehog(“Hhf”). The extracellular signal, Hh, has been shown to controlexpression of TGF-beta, Wnt and FGF signalling molecules, and initiateboth short-range and long-range signalling actions. A short-range actionof Hh in Drosophila, for example, is found in the ventral epidermis,where Hh is associated with causing adjacent cells to maintain wingless(wg) expression [Perrimon, Cell, 76:781-784 (1984)]. In the vertebratecentral nervous system, for example, Sonic hedgehog (“SHh”; a secretedvertebrate homologue of dHh) is expressed in notocord cells and isassociated with inducing floor plate formation within the adjacentneural tube in a contact-dependent manner [Roelink et al., Cell,76:761-775 (1994)]. Perrimon, Cell, 80:517-520 (1995) provide a generalreview of some of the long-range actions associated with Hh.

Studies of the Hh protein in Drosophila (“dHh”) have shown that Hhencodes a 46 kDa native protein that is cleaved into a 39 kDa formfollowing signal sequence cleavage and subsequently cleaved into a 19kDa amino-terminal form and a 26 kDa carboxy-terminal form [Lee et al.,Science, 266:1528-1537 (1994)]. Lee et al. report that the 19 kDa and 26kDa forms have different biochemical properties and are differentiallydistributed. DiNardo et al. and others have disclosed that the dHhprotein triggers a signal transduction cascade that activates wg[DiNardo et al., Nature, 332:604-609 (1988); Hidalgo and Ingham,Development, 110:291-301 (1990); Ingham and Hidalgo, Development,117:283-291 (1993)] and at least another segment polarity gene, patched(ptc) [Hidalgo and Ingham, supra; Tabata and Komberg, Cell, 76:89-102(1994)]. Properties and characteristics of dHh are also described inreviews by Ingham et al., Curr. Opin. Genet. Dev., 5:492-498 (1995) andLuinsden and Graham et al., Curr. Biol., 5:1347-1350 (1995). Propertiesand characteristics of the vertebrate homologue of dHh, Sonic hedgehog,are described by Echelard et al., Cell, 75:1417-1430 (1993); Krauss etal., Cell, 75:1431-1444 (1993); Riddle et al., Cell, 75:1401-1416(1993); Johnson et al., Cell, 79:1165-1173 (1994); Fan et al., Cell,81:457-465 (1995); Roberts et al., Development, 121:3163-3174 (1995);and Hynes et al., Cell, 80:95-101 (1995).

In Perrimon, Cell, 80:517-520 (1995), it was reported that thebiochemical mechanisms and receptors by which signalling molecules likeWg and. Hh regulate the activities, transcription, or both, of secondarysignal transducers have generally not been well understood. InDrosophila, genetic evidence indicates that Frizzled (“Fz”) functions totransmit and transduce polarity signals in epidermal cells during hairand bristle development. Fz rat homologues which have structuralsimilarity with members of the G-protein-coupled receptor superfamilyhave been described by Chan et al., J. Biol. Chem., 267:25202-25207(1992). Specifically, Chan et al. describe isolating two different cDNAsfrom a rat cell library, the first cDNA encoding a predicted 641 residueprotein, Fz-1, having 46% homology with Drosophila Fz, and a second cDNAencoding a protein, Fz-2, of 570 amino acids that is 80% homologous withFz-1. Chan et al. state that mammalian fz may constitute a gene familyimportant for transduction and intercellular transmission of polarityinformation during tissue morphogenesis or in differentiated tissues.Recently, Bhanot et al. did describe the identification of a Drosophilagene, frizzled2 (Dfz2), and predicted Dfz2 protein, which can functionas a wg receptor in cultured cells [Bhanot et al., Nature, 382:225-230(1996)]. Bhanot et al. disclose, however, that there is no in vivoevidence that shows Dfz2 is required for Wg signalling.

Although some evidence suggests that cellular responses to dHh aredependent on the transmembrane protein, smoothened (dSmo),[Nusslein-Volhard et al., Wilhelm Roux's Arch. Dev. Biol., 193:267-282(1984); Jurgens et al., Wilhelm Roux's Arch. Dev. Biol., 193:283-295(1984); Alcedo et al., Cell, 86:221-232 (Jul. 26, 1996); van den Heuveland Ingham, Nature, 382:547-551 (Aug. 8, 1996)], and are negativelyregulated by the transmembrane protein, “Patched” [(Hooper and Scott,Cell, 59:751-765 (1989); Nakano et al., Nature, 341:508-513 (1989);Hidalgo and Ingham, supra; Ingham et al., Nature, 353:184-187 (1991)],the receptors for Hh proteins have not previously been biochemicallycharacterized. Various gene products, including the Patched protein, thetranscription factor cubitus interruptus, the serine/threonine kinase“fused”, and the gene products of Costal-2, smoothened (smo) andSuppressor of fused (Su(fu)), have been implicated as putativecomponents of the Hh signalling pathway.

Prior studies in Drosophila led to the hypothesis that ptc encoded theHh receptor [Ingham et al., Nature, 353:184-187 (1991)]. The activity ofthe ptc product, which is a multiple membrane spanning cell surfaceprotein referred to as Patched [Hooper and Scott, supra], represses thewg and ptc genes and is antagonized by the Hh signal. Patched wasproposed by Ingham et al. to be a constitutively active receptor whichis inactivated by binding of Hh, thereby permitting transcription ofHh-responsive genes. As reported by Bejsovec and Wieschaus, Development,119:501-517 (1993), however, Hh has effects in ptc null Drosophilaembryos and thus cannot be the only Hh receptor. Accordingly, the roleof Patched in Hh signalling has not been fully understood.

Goodrich et al. have isolated a murine patched gene [Goodrich et al.,Genes Dev., 10:301-312 (1996)]. Human patched homologues have also beendescribed in recently published literature. For instance, Hahn et al.,Cell, 85:841-851 (1996) describe isolation of a human homolog ofDrosophila ptc. The gene displays up to 67% sequence identity at thenucleotide level and 60% similarity at the amino acid level with theDrosophila gene [Hahn et al., supra]. Johnson et al. also provide apredicted amino acid sequence of a human Patched protein [Johnson etal., Science, 272:1668-1671 (1996)]. Johnson et al. disclose that the1447 amino acid protein has 96% and 40% identity to mouse and DrosophilaPatched, respectively. The human and mouse data from these investigatorssuggest that patched is a single copy gene in mammals. According to Hahnet al., Cell, 85:841-851 (1996), analyses revealed the presence of threedifferent 5′ ends for their human ptc gene. Hahn et al. postulate theremay be at least three different forms of the Patched protein inmammalian cells: the ancestral form represented by the murine sequence,and the two human forms. Patched is further discussed in a recent reviewby Marigo et al., Development, 122:1225 (1996).

Studies in Drosophila have also led to the hypothesis that Smo could bea candidate receptor for Hh [Alcedo et al., supra; van den Heuvel andIngham, supra]. The smoothened (smo) gene was identified as a segmentpolarity gene and initially named smooth [Nusslein-Volhard et al.,supra]. Since that name already described another locus, though, thesegment polarity gene was renamed smoothened [Lindsley and Zimm, “TheGenome of Drosophila melanogaster,” San Diego, Calif.:Academic Press(1992)]. As first reported by Nusslein-Volhard et al., supra, the smogene is required for the maintenance of segmentation in Drosophilaembryos.

Alcedo et al., supra, have recently described the cloning of theDrosophila smoothened gene [see also, van den Heuvel and Ingham, supra].Alcedo et al. report that hydropathy analysis predicts that the putativeSmo protein is an integral membrane protein with seven membrane spanningalpha helices, a hydrophobic segment near the N-terminus, and ahydrophilic C-terminal tail. Thus, Smo may belong to the serpentinereceptor family, whose members are all coupled to G proteins. Alcedo etal., supra, also report that smo is necessary for Hh signalling and thatit acts downstream of hh and ptc.

As discussed in Pennisi, Science, 272:1583-1584 (1996), certaindevelopment genes are believed to play some role in cancer because theycontrol cell growth and specialization. Recent studies suggest thatpatched is a tumor suppressor, or a gene whose loss or inactivationcontributes to the excessive growth of cancer cells. Specifically, Hahnet al. and other investigators have found that patched is mutated insome common forms of basal cell carcinomas in humans [Hahn et al., Cell,85:841-851 (1996); Johnson et al., supra; Gailani et al., in Letters,Nature Genetics, 13:September, 1996]. Hahn et al. report thatalterations predicted to inactivate the patched gene product were foundin six unrelated patients having basal cell nevus syndrome (“BCNS”), afamilial complex of cancers and developmental abnormalities. Hahn et al.also report that the ptc pathway has been implicated in tumorigenesis bythe cloning of the pancreatic tumor suppressor gene, DPC4. Vertebratehomologues of two other Drosophila segment polarity genes, the murinemammary Wntl [Rijsewijk et al., Cell, 50:649 (1987)] and the humanglioblastoma GLI [Kinzler et al., Science, 236:70 (1987)], have alsobeen implicated in cancer.

SUMMARY OF THE INVENTION

Applicants have identified cDNA clones that encode novel vertebrateSmoothened proteins, designated herein as “vSmo.” In particular, cDNAclones encoding rat Smoothened and human Smoothened have beenidentified. The vSmo proteins of the invention have surprisingly beenfound to be co-expressed with Patched proteins and to form physicalcomplexes with Patched. Applicants also discovered that the vSmo alonedid not bind Sonic hedgehog but that vertebrate Patched homologues didbind Sonic hedgehog with relatively high affinity. It is believed thatSonic hedgehog may mediate its biological activities through amulti-subunit receptor in which vSmo is a signalling component andPatched is a ligand binding component, as well as a ligand regulatedsuppressor of vSmo. Accordingly, without being limited to any onetheory, pathological conditions, such as basal cell carcinoma,associated with inactivated (or mutated) Patched may be the result ofconstitutive activity of vSmo or vSmo signalling following from negativeregulation by Patched.

In one embodiment, the invention provides isolated vertebrateSmoothened. In particular, the invention provides isolated nativesequence vertebrate Smoothened, which in one embodiment, includes anamino acid sequence comprising residues 1 to 793 of FIG. 1 (SEQ IDNO:2). The invention also provides isolated native sequence vertebrateSmoothened which includes an amino acid sequence comprising residues 1to 787 of FIG. 4 (SEQ ID NO:4). In other embodiments, the isolatedvertebrate Smoothened comprises at least about 80% identity with nativesequence vertebrate Smoothened comprising residues 1 to 787 of FIG. 4(SEQ ID NO:4).

In another embodiment, the invention provides chimeric moleculescomprising vertebrate Smoothened fused to a heterologous polypeptide oramino acid sequence. An example of such a chimeric molecule comprises avertebrate Smoothened fused to an epitope tag sequence.

In another embodiment, the invention provides an isolated nucleic acidmolecule encoding vertebrate Smoothened. In one aspect, the nucleic acidmolecule is RNA or DNA that encodes a vertebrate Smoothened, or iscomplementary to such encoding nucleic acid sequence, and remains stablybound to it under stringent conditions. In one embodiment, the nucleicacid sequence is selected from:

(a) the coding region of the nucleic acid sequence of FIG. 1 (SEQ IDNO:1) that codes for residue 1 to residue 793 (i.e., nucleotides 450-452through 2826-2828), inclusive;

(b) the coding region of the nucleic acid sequence of FIG. 4 (SEQ IDNO:3) that codes for residue 1 to residue 787 (i.e., nucleotides 13-15through 2371-2373), inclusive; or

(c) a sequence corresponding to the sequence of (a) or (b) within thescope of degeneracy of the genetic code.

In a further embodiment, the invention provides a vector comprising thenucleic acid molecule encoding the vertebrate Smoothened. A host cellcomprising the vector or the nucleic acid molecule is also provided. Amethod of producing vertebrate Smoothened is further provided.

In another embodiment, the invention provides an antibody whichspecifically binds to vertebrate Smoothened. The antibody may be anagonistic, antagonistic or neutralizing antibody.

In another embodiment, the invention provides non-human, transgenic orknock-out animals.

Another embodiment of the invention provides articles of manufacture andkits that include vertebrate Smoothened or vertebrate Smoothenedantibodies.

A further embodiment of the invention provides protein complexescomprising vertebrate Smoothened protein and vertebrate Patched protein.In one embodiment the complexes further include vertebrate Hedgehogprotein. The invention also provides vertebrate Patched which binds tovertebrate Smoothened. Optionally, the vertebrate Patched comprises asequence which is a derivative of or fragment of a native sequencevertebrate Patched.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1F show the nucleotide (SEQ ID NO:1) and deduced amino acidsequence (SEQ ID NO:2) of native sequence rat Smoothened.

FIGS. 2A-2B show the primary structure of rat Smo (rSmo) (SEQ ID NO:2)and Drosophila Smo (dsmo)(SEQ ID NO:5). The signal peptide sequences areunderlined, conserved amino acids are boxed, cysteines are marked withasterisks, potential glycosylation sites are marked with dashed boxes,and the seven hydrophobic transmembrane domains are shaded.

FIGS. 3A-3O show the tissue distribution of SHH, Smo and Patched inembryonic and adult rat tissues. In situ hybridization of SHH (leftcolumn); Smo (middle column) and Patched (right column, not includinginsets) to rat tissues. Row E15 Sag, sagittal sections through E15 ratembryos. Rows E9, E10, E12, and E15, coronal sections through E9 neuralfolds. E10 neural tube and somites, E12 and E15 neural tube. Insets inRow E12 show sections through forelimb bud of E12 rat embryos.Legend—ht=heart; sk=skin; bl=bladder; ts=testes; lu=lung; to=tongue;vtc=vertebral column; nf=neural fold; nc=notocord; so=somite; fp=floorplate; vh=ventral horn; vz=ventricular zone; cm=cardiac mesoderm andvm=ventral midbrain.

FIGS. 4A-4E show the nucleotide (SEQ ID NO:3) and deduced amino acidsequence (SEQ ID NO:4) for native sequence human Smoothened.

FIGS. 5A-5E show the primary structure of human Smo (hSmo) (SEQ ID NO:4)and rat Smo (rat.Smo) (SEQ ID NO:2) and homology to Drosophila Smo(dros.smo)(SEQ ID NO:5). Conserved amino acids are boxed.

FIGS. 6A-6I illustrate the results of binding and co-immunoprecipitationassays which show SHH-N binds to mPatched but not to rSmo. Staining ofcells expressing the Flag tagged rSmo (a and b) or Myc tagged mPatched(c, d, and e) with (a) Flag (Smo) antibody; (c) Myc (mPatched) antibody;(b and d) IgG-SHH-N; or (e) Flag tagged SHH-N. (f)Co-immunoprecipitation of epitope tagged mPatched (Patched) or epitopetagged rSmo (Smo) with IgG-SHH-N. (g) cross-linking of ¹²⁵I-SHH-N(¹²⁵I-SHH) to cells expressing mPatched or rSmo in the absence orpresence of unlabeled SHH-N. (h) Co-immunoprecipitation of ¹²⁵I-SHH byan epitope tagged mPatched (Patched) or an epitope tagged rSmo (Smo).(i) competition binding of ¹²⁵I-SHH to cells expressing mPatched ormPatched plus rSmo.

FIGS. 7A-7E illustrate (a) Double immunohistochemical staining ofPatched (red) and Smo (green) in transfected cells. Yellow indicatesco-expression of the two proteins; (b and c) Detection of Patched-SmoComplex by immunoprecipitation; (b) immunoprecipitation with antibodiesto the epitope tagged Patched and analysis on a Western blot withantibodies to epitope tagged Smo; (c) immunoprecipitation withantibodies to the epitope tagged Smo and analysis on a Western blot withantibodies to epitope tagged Patched; (d and e) co-immunoprecipitationof ¹²⁵I-SHH bound to cells expressing both Smo and Patched withantibodies to either Smo (d) or Patched (e) epitope tags.

FIG. 8 shows a Western blot from a SDS-gel depicting the expressionlevel of a wildtype (WT) and mutated Patched (mutant).

FIG. 9 shows a model describing the putative SHH receptor and itsproposed activation by SHH. As shown in the model, Patched is a ligandbinding component and vSmo is a signalling component in a multi-subunitSHH receptor.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

I. Definitions

The terms “vertebrate Smoothened”, “vertebrate Smoothened protein” and“vSmo” when used herein encompass native sequence vertebrate Smoothenedand vertebrate Smoothened variants (each of which is defined herein).These terms encompass Smoothened from a variety of animals classified asvertebrates, including mammals. In a preferred embodiment, thevertebrate Smoothened is rat Smoothened (rSmo) or human Smoothened(hSmo). The vertebrate Smoothened may be isolated from a variety ofsources, such as from human tissue types or from another source, orprepared by recombinant or synthetic methods.

A “native sequence vertebrate Smoothened” comprises a protein having thesame amino acid sequence as a vertebrate Smoothened derived from nature.Thus, a native sequence vertebrate Smoothened can have the amino acidsequence of naturally occurring human Smoothened, rat Smoothened, orSmoothened from any other vertebrate. Such native sequence vertebrateSmoothened can be isolated from nature or can be produced by recombinantor synthetic means. The term “native sequence vertebrate Smoothened”specifically encompasses naturally-occurring truncated forms of thevertebrate Smoothened, naturally-occurring variant forms (e.g.,alternatively spliced forms) and naturally-occurring allelic variants ofthe vertebrate Smoothened. In one embodiment of the invention, thenative sequence vertebrate Smoothened is a mature native sequenceSmoothened comprising the amino acid sequence of SEQ ID NO:4. In anotherembodiment of the invention, the native sequence vertebrate Smoothenedis a mature native sequence Smoothened comprising the amino acidsequence of SEQ ID NO:2.

“Vertebrate Smoothened variant” means a vertebrate Smoothened as definedbelow having less than 100% sequence identity with vertebrate Smoothenedhaving the deduced amino acid sequence shown in SEQ ID NO:4 for humanSmoothened or SEQ ID NO:2 for rat Smoothened. Such vertebrate Smoothenedvariants include, for instance, vertebrate Smoothened proteins whereinone or more amino acid residues are added at the N- or C-terminus of, orwithin, the sequences of SEQ ID NO:4 or SEQ ID NO:2; wherein about oneto thirty amino acid residues are deleted, or optionally substituted byone or more amino acid residues; and derivatives thereof, wherein anamino acid residue has been covalently modified so that the resultingproduct has a non-naturally occurring amino acid. Ordinarily, avertebrate Smoothened variant will have at least about 80% sequenceidentity, more preferably at least about 90% sequence identity, and evenmore preferably at least about 95% sequence identity with the sequenceof SEQ ID NO:4 or SEQ ID NO:2.

The term “epitope tag” when used herein refers to a tag polypeptidehaving enough residues to provide an epitope against which an antibodythereagainst can be made, yet is short enough such that it does notinterfere with activity of the vertebrate Smoothened. The tagpolypeptide preferably also is fairly unique so that the antibodythereagainst does not substantially cross-react with other epitopes.Suitable tag polypeptides generally have at least six amino acidresidues and usually between about 8-50 amino acid residues (preferablybetween about 9-30 residues).

“Isolated,” when used to describe the various proteins disclosed herein,means protein that has been identified and separated and/or recoveredfrom a component of its natural environment. Contaminant components ofits natural environment are materials that would typically interferewith diagnostic or therapeutic uses for the protein, and may includeenzymes, hormones, and other proteinaceous or non-proteinaceoussubstances. In preferred embodiments, the protein will be purified (1)to a degree sufficient to obtain at least 15 residues of N-terminal orinternal amino acid sequence by use of a spinning cup sequenator, or (2)to homogeneity by SDS-PAGE under non-reducing or reducing conditionsusing Coomassie blue or, preferably, silver stain. Isolated proteinincludes protein in situ within recombinant cells, since at least onecomponent of the vSmo natural environment will not be present.Ordinarily, however, isolated protein will be prepared by at least onepurification step.

An “isolated” vSmo nucleic acid molecule is a nucleic acid molecule thatis identified and separated from at least one contaminant nucleic acidmolecule with which it is ordinarily associated in the natural source ofthe vSmo nucleic acid. An isolated vSmo nucleic acid molecule is otherthan in the form or setting in which it is found in nature. IsolatedvSmo nucleic acid molecules therefore are distinguished from the vSmonucleic acid molecule as it exists in natural cells. However, anisolated vSmo nucleic acid molecule includes vSmo nucleic acid moleculescontained in cells that ordinarily express vSmo where, for example, thenucleic acid molecule is in a chromosomal location different from thatof natural cells.

The term “control sequences” refers to DNA sequences necessary for theexpression of an operably linked coding sequence in a particular hostorganism. The control sequences that are suitable for prokaryotes, forexample, include a promoter, optionally an operator sequence, and aribosome binding site. Eukaryotic cells are known to utilize promoters,polyadenylation signals, and enhancers.

Nucleic acid is “operably linked” when it is placed into a functionalrelationship with another nucleic acid sequence. For example, DNA for apresequence or secretory leader is operably linked to DNA for apolypeptide if it is expressed as a preprotein that participates in thesecretion of the polypeptide; a promoter or enhancer is operably linkedto a coding sequence if it affects the transcription of the sequence; ora ribosome binding site is operably linked to a coding sequence if it ispositioned so as to facilitate translation. Generally, “operably linked”means that the DNA sequences being linked are contiguous, and, in thecase of a secretory leader, contiguous and in reading phase. However,enhancers do not have to be contiguous. Linking is accomplished byligation at convenient restriction sites. If such sites do not exist,the synthetic oligonucleotide adaptors or linkers are used in accordancewith conventional practice.

The term “antibody” is used in the broadest sense and specificallycovers single anti-vSmo monoclonal antibodies (including agonist,antagonist, and neutralizing antibodies) and anti-vSmo antibodycompositions with polyepitopic specificity.

The term “monoclonal antibody” as used herein refers to an antibodyobtained from a population of substantially homogeneous antibodies,i.e., the individual antibodies comprising the population are identicalexcept for possible naturally-occurring mutations that may be present inminor amounts. Monoclonal antibodies are highly specific, being directedagainst a single antigenic site. Furthermore, in contrast toconventional (polyclonal) antibody preparations which typically includedifferent antibodies directed against different determinants (epitopes),each monoclonal antibody is directed against a single determinant on theantigen.

The monoclonal antibodies herein include hybrid and recombinantantibodies produced by splicing a variable (including hypervariable)domain of an anti-vSmo antibody with a constant domain (e.g. “humanized”antibodies), or a light chain with a heavy chain, or a chain from onespecies with a chain from another species, or fusions with heterologousproteins, regardless of species of origin or immunoglobulin class orsubclass designation, as well as antibody fragments (e.g., Fab, F(ab′)₂,and Fv), so long as they exhibit the desired activity. See, e. g. U.S.Pat. No. 4,816,567 and Mage et al., in Monoclonal Antibody ProductionTechniques and Applications, pp. 79-97 (Marcel Dekker, Inc.: New York,1987).

Thus, the modifier “monoclonal” indicates the character of the antibodyas being obtained from a substantially homogeneous population ofantibodies, and is not to be construed as requiring production of theantibody by any particular method. For example, the monoclonalantibodies to be used in accordance with the present invention may bemade by the hybridoma method first described by Kohler and Milstein,Nature, 256:495 (1975), or may be made by recombinant DNA methods suchas described in U.S. Pat. No. 4,816,567. The “monoclonal antibodies” mayalso be isolated from phage libraries generated using the techniquesdescribed in McCafferty et al., Nature, 348:552-554 (1990), for example.

“Humanized” forms of non-human (e.g. murine) antibodies are specificchimeric immunoglobulins, immunoglobulin chains, or fragments thereof(such as Fv, Fab, Fab′, F(ab′)₂ or other antigen-binding subsequences ofantibodies) which contain minimal sequence derived from non-humanimmunoglobulin. For the most part, humanized antibodies are humanimmunoglobulins (recipient antibody) in which residues from acomplementary determining region (CDR) of the recipient are replaced byresidues from a CDR of a non-human species (donor antibody) such asmouse, rat, or rabbit having the desired specificity, affinity, andcapacity. In some instances, Fv framework region (FR) residues of thehuman immunoglobulin are replaced by corresponding non-human residues.Furthermore, the humanized antibody may comprise residues which arefound neither in the recipient antibody nor in the imported CDR orframework sequences. These modifications are made to further refine andoptimize antibody performance. In general, the humanized antibody willcomprise substantially all of at least one, and typically two, variabledomains, in which all or substantially all of the CDR regions correspondto those of a non-human immunoglobulin and all or substantially all ofthe FR regions are those of a human immunoglobulin consensus sequence.The humanized antibody optimally also will comprise at least a portionof an immunoglobulin constant region or domain (Fc), typically that of ahuman immunoglobulin.

The term “vertebrate” as used herein refers to any animal classified asa vertebrate including certain classes of fish, reptiles, birds, andmammals. The term “mammal” as used herein refers to any animalclassified as a mammal, including humans, cows, rats, mice, horses, dogsand cats.

II. Modes For Carrying Out the Invention

The present invention is based on the discovery of vertebrate homologuesof Smoothened. In particular, Applicants have identified and isolatedhuman and rat Smoothened. The properties and characteristics of humanand rat Smoothened are described in further detail in the Examplesbelow. Based upon the properties and characteristics of human and ratSmoothened disclosed herein, it is Applicants' present belief thatvertebrate Smoothened is a signalling component in a multi-subunitHedgehog (particularly Sonic Hedgehog “SHH”) receptor.

A description follows as to how vertebrate Smoothened may be prepared.

A. Preparation of vSmo

Techniques suitable for the production of vSmo are well known in the artand include isolating vSmo from an endogenous source of the polypeptide,peptide synthesis (using a peptide synthesizer) and recombinanttechniques (or any combination of these techniques). The descriptionbelow relates primarily to production of vSmo by culturing cellstransformed or transfected with a vector containing vSmo nucleic acid.It is of course, contemplated that alternative methods, which are wellknown in the art, may be employed to prepare vSmo.

1. Isolation of DNA Encoding vSmo

The DNA encoding vSmo may be obtained from any cDNA library preparedfrom tissue believed to possess the vSmo mRNA and to express it at adetectable level. Accordingly, human Smo DNA can be convenientlyobtained from a cDNA library prepared from human tissues, such as thelibrary of human embryonic lung cDNA described in Example 3. Rat Smo DNAcan be conveniently obtained from a cDNA library prepared from rattissues, such as described in Example 1. The vsmo-encoding gene may alsobe obtained from a genomic library or by oligonucleotide synthesis.

Libraries can be screened with probes (such as antibodies to the vSmo oroligonucleotides or polypeptides as described in the Examples) designedto identify the gene of interest or the protein encoded by it. Theprobes are preferably labeled such that they can be detected uponhybridization to DNA in the library being screened. Methods of labelingare well known in the art, and include the use of radiolabels like³²P-labeled ATP, biotinylation or enzyme labeling. Screening the cDNA orgenomic library with a selected probe may be conducted using standardprocedures, such as described in Sambrook et al., Molecular Cloning: ALaboratory Manual (New York: Cold Spring Harbor Laboratory Press, 1989).An alternative means to isolate the gene encoding vSmo is to use PCRmethodology [Sambrook et al., supra; Dieffenbach et al., PCR Primer:ALaboratory Manual (Cold Spring Harbor Laboratory Press, 1995)].

Nucleic acid having all the protein coding sequence may be obtained byscreening selected cDNA or genomic libraries using the deduced aminoacid sequences disclosed herein, and, if necessary, using conventionalprimer extension procedures as described in Sambrook et al., supra, todetect precursors and processing intermediates of mRNA that may not havebeen reverse-transcribed into cDNA.

vSmo variants can be prepared by introducing appropriate nucleotidechanges into the vSmo DNA, or by synthesis of the desired vSmopolypeptide. Those skilled in the art will appreciate that amino acidchanges (compared to native sequence vSmo) may alter post-translationalprocesses of the vSmo, such as changing the number or position ofglycosylation sites.

Variations in the native sequence vSmo can be made using any of thetechniques and guidelines for conservative and non-conservativemutations set forth in U.S. Pat. No. 5,364,934. These includeoligonucleotide-mediated (site-directed) mutagenesis, alanine scanning,and PCR mutagenesis.

2. Insertion of Nucleic Acid Into a Replicable Vector

The nucleic acid (e.g., cDNA or genomic DNA) encoding vSmo may beinserted into a replicable vector for further cloning (amplification ofthe DNA) or for expression. Various vectors are publicly available. Thevector components generally include, but are not limited to, one or moreof the following: a signal sequence, an origin of replication, one ormore marker genes, an enhancer element, a promoter, and a transcriptiontermination sequence, each of which is described below.

(i) Signal Sequence Component

The vSmo may be produced recombinantly not only directly, but also as afusion polypeptide with a heterologous amino acid sequence orpolypeptide, which may be a signal sequence or other polypeptide havinga specific cleavage site at the N-terminus of the mature protein orpolypeptide. In general, the signal sequence may be a component of thevector, or it may be a part of the vSmo DNA that is inserted into thevector. The heterologous signal sequence selected preferably is one thatis recognized and processed (i.e., cleaved by a signal peptidase) by thehost cell.

(ii) Origin of Replication Component

Both expression and cloning vectors contain a nucleic acid sequence thatenables the vector to replicate in one or more selected host cells.Generally, in cloning vectors this sequence is one that enables thevector to replicate independently of the host chromosomal DNA, andincludes origins of replication or autonomously replicating sequences.Such sequences are well known for a variety of bacteria, yeast, andviruses.

Most expression vectors are “shuttle” vectors, i.e., they are capable ofreplication in at least one class of organisms but can be transfectedinto another organism for expression. For example, a vector is cloned inE. coli and then the same vector is transfected into yeast or mammaliancells for expression even though it is not capable of replicatingindependently of the host cell chromosome.

DNA may also be amplified by insertion into the host genome. This isreadily accomplished using Bacillus species as hosts, for example, byincluding in the vector a DNA sequence that is complementary to asequence found in Bacillus genomic DNA. Transfection of Bacillus withthis vector results in homologous recombination with the genome andinsertion of vSmo DNA.

(iii) Selection Gene Component

Expression and cloning vectors typically contain a selection gene, alsotermed a selectable marker. This gene encodes a protein necessary forthe survival or growth of transformed host cells grown in a selectiveculture medium. Host cells not transformed with the vector containingthe selection gene will not survive in the culture medium. Typicalselection genes encode proteins that (a) confer resistance toantibiotics or other toxins, e.g., ampicillin, neomycin, methotrexate,or tetracycline, (b) complement auxotrophic deficiencies, or (c) supplycritical nutrients not available from complex media, e.g., the geneencoding D-alanine racemase for Bacilli.

One example of a selection scheme utilizes a drug to arrest growth of ahost cell. Those cells that are successfully transformed with aheterologous gene produce a protein conferring drug resistance and thussurvive the selection regimen. Examples of such dominant selection usethe drugs neomycin [Southern et al., J. Molec. Appl. Genet., 1:327(1982)], mycophenolic acid (Mulligan et al., Science, 209:1422 (1980)]or hygromycin [Sugden et al., Mol. Cell. Biol., 5:410-413 (1985)]. Thethree examples given above employ bacterial genes under eukaryoticcontrol to convey resistance to the appropriate drug G418 or neomycin(geneticin), xgpt (mycophenolic acid), or hygromycin, respectively.

Another example of suitable selectable markers for mammalian cells arethose that enable the identification of cells competent to take up thevSmo nucleic acid, such as DHFR or thymidine kinase. The mammalian celltransformants are placed under selection pressure that only thetransformants are uniquely adapted to survive by virtue of having takenup the marker. Selection pressure is imposed by culturing thetransformants under conditions in which the concentration of selectionagent in the medium is successively changed, thereby leading toamplification of both the selection gene and the DNA that encodes vSmo.Amplification is the process by which genes in greater demand for theproduction of a protein critical for growth are reiterated in tandemwithin the chromosomes of successive generations of recombinant cells.

Cells transformed with the DHFR selection gene may first be identifiedby culturing all of the transformants in a culture medium that containsmethotrexate (Mtx), a competitive antagonist of DHFR. An appropriatehost cell when wild-type DHFR is employed is the Chinese hamster ovary(CHO) cell line deficient in DHFR activity, prepared and propagated asdescribed by Urlaub et al., Proc. Natl. Acad. Sci. USA, 77:4216 (1980).The transformed cells are then exposed to increased levels ofmethotrexate. This leads to the synthesis of multiple copies of the DHFRgene, and, concomitantly, multiple copies of other DNA comprising theexpression vectors, such as the DNA encoding vSmo.

(iv) Promoter Component

Expression and cloning vectors usually contain a promoter that isrecognized by the host organism and is operably linked to the vSmonucleic acid sequence. Promoters are untranslated sequences locatedupstream (5′) to the start codon of a structural gene (generally withinabout 100 to 1000 bp) that control the transcription and translation ofparticular nucleic acid sequence, such as the vSmo nucleic acidsequence, to which they are operably linked. Such promoters typicallyfall into two classes, inducible and constitutive. Inducible promotersare promoters that initiate increased levels of transcription from DNAunder their control in response to some change in culture conditions,e.g., the presence or absence of a nutrient or a change in temperature.At this time a large number of promoters recognized by a variety ofpotential host cells are well known. These promoters are operably linkedto vSmo encoding DNA by removing the promoter from the source DNA byrestriction enzyme digestion and inserting the isolated promotersequence into the vector.

Promoters suitable for use with prokaryotic hosts include theβ-lactamase and lactose promoter systems [Chang el al., Nature,275:617-624 (1978); Goeddel et al., Nature, 281:544 (1979)], alkalinephosphatase, a tryptophan (trp) promoter system [Goeddel, Nucleic AcidsRes., 8:4057 (1980); EP 36,776], and hybrid promoters such as the tacpromoter [deBoer et al, Proc. Natl. Acad. Sci. USA, 80:21-25 (1983)].

Promoter sequences are known for eukaryotes. Virtually all eukaryoticgenes have an AT-rich region located approximately 25 to 30 basesupstream from the site where transcription is initiated. Anothersequence found 70 to 80 bases upstream from the start of transcriptionof many genes is a CXCAAT region where X may be any nucleotide. At the3′ end of most eukaryotic genes is an AATAAA sequence that may be thesignal for addition of the poly A tail to the 3′ end of the codingsequence. All of these sequences are suitably inserted into eukaryoticexpression vectors.

Examples of suitable promoting sequences for use with yeast hostsinclude the promoters for 3-phosphoglycerate kinase [Hitzeman et al., J.Biol. Chem., 255:12073-12080 (1980)] or other glycolytic enzymes [Hesset al., J. Adv. Enzyme Reg., 7:149 (1968); Holland, Biochemistry,17:4900 (1978)], such as enolase, glyceraldehyde-3-phosphatedehydrogenase, hexokinase, pyruvate decarboxylase, phosphofructokinase,glucose-6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvatekinase, triosephosphate isomerase, phosphoglucose isomerase, andglucokinase. Suitable vectors and promoters for use in yeast expressionare further described in EP 73,657.

vSmo transcription from vectors in mammalian host cells is controlled,for example, by promoters obtained from the genomes of viruses such aspolyoma virus, fowlpox virus (UK 2,211,504 published Jul. 5, 1989),adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcomavirus, cytomegalovirus, a retrovirus, hepatitis-B virus and mostpreferably Simian Virus 40 (SV40), from heterologous mammalianpromoters, e.g., the actin promoter or an immunoglobulin promoter.

The early and late promoters of the SV40 virus are conveniently obtainedas an SV40 restriction fragment that also contains the SV40 viral originof replication [Fiers et al., Nature, 273:113 (1978); Mulligan and Berg,Science, 209:1422-1427 (1980); Pavlakis et al., Proc. Natl. Acad. Sci.USA, 78:7398-7402 (1981)]. The immediate early promoter of the humancytomegalovirus is conveniently obtained as a HindIII E restrictionfragment [Greenaway et al., Gene, 18:355-360 (1982)]. A system forexpressing DNA in mammalian hosts using the bovine papilloma virus as avector is disclosed in U.S. Pat. No. 4,419,446. A modification of thissystem is described in U.S. Pat. No. 4,601,978 [See also Gray et al.,Nature, 295:503-508 (1982) on expressing cDNA encoding immune interferonin monkey cells; Reyes et al., Nature, 297:598-601 (1982) on expressionof human β-interferon cDNA in mouse cells under the control of athymidine kinase promoter from herpes simplex virus; Canaani and Berg,Proc. Natl. Acad. Sci. USA 79:5166-5170 (1982) on expression of thehuman interferon β1 gene in cultured mouse and rabbit cells; and Gormanet al., Proc. Natl. Acad. Sci. USA, 79:6777-6781 (1982) on expression ofbacterial CAT sequences in CV-1 monkey kidney cells, chicken embryofibroblasts, Chinese hamster ovary cells, HeLa cells, and mouse NIH-3T3cells using the Rous sarcoma virus long terminal repeat as a promoter].

(v) Enhancer Element Component

Transcription of a DNA encoding the vSmo by higher eukaryotes may beincreased by inserting an enhancer sequence into the vector. Enhancersare cis-acting elements of DNA, usually about from 10 to 300 bp, thatact on a promoter to increase its transcription. Enhancers arerelatively orientation and position independent, having been found 5′[Laimins et al., Proc. Natl. Acad. Sci. USA, 78:464-468 (1981]) and 3′[Lusky el al., Mol. Cell Bio., 3:1108 (1983]) to the transcription unit,within an intron [Banerji el al., Cell. 33:729 (1983)], as well aswithin the coding sequence itself [Osborne et al., Mol. Cell Bio.,4:1293 (1984)]. Many enhancer sequences are now known from mammaliangenes (globin, elastase, albumin, α-fetoprotein, and insulin).Typically, however, one will use an enhancer from a eukaryotic cellvirus. Examples include the SV40 enhancer on the late side of thereplication origin (bp 100-270), the cytomegalovirus early promoterenhancer, the polyoma enhancer on the late side of the replicationorigin, and adenovirus enhancers. See also Yaniv, Nature, 297:17-18(1982) on enhancing elements for activation of eukaryotic promoters.

(vi) Transcription Termination Component

Expression vectors used in eukaryotic host cells (yeast, fungi, insect,plant, animal, human, or nucleated cells from other multicellularorganisms) will also typically contain sequences necessary for thetermination of transcription and for stabilizing the mRNA. Suchsequences are commonly available from the 5′ and, occasionally 3′,untranslated regions of eukaryotic or viral DNAs or cDNAs. These regionscontain nucleotide segments transcribed as polyadenylated fragments inthe untranslated portion of the mRNA encoding vSmo.

(vii) Construction and Analysis of Vectors

Construction of suitable vectors containing one or more of theabove-listed components employs standard ligation techniques. Isolatedplasmids or DNA fragments are cleaved, tailored, and re-ligated in theform desired to generate the plasmids required.

For analysis to confirm correct sequences in plasmids constructed, theligation mixtures can be used to transform E. coli K12 strain 294 (ATCC31,446) and successful transformants selected by ampicillin ortetracycline resistance where appropriate. Plasmids from thetransformants are prepared, analyzed by restriction endonucleasedigestion, and/or sequenced by the method of Messing et al., NucleicAcids Res., 9:309 (1981) or by the method of Maxam et al., Methods inEnzymology, 65:499. (1980).

(viii) Transient Expression Vectors

Expression vectors that provide for the transient expression inmammalian cells of DNA encoding vSmo may be employed. In general,transient expression involves the use of an expression vector that isable to replicate efficiently in a host cell, such that the host cellaccumulates many copies of the expression vector and, in turn,synthesizes high levels of a desired polypeptide encoded by theexpression vector [Sambrook et al., supra]. Transient expressionsystems, comprising a suitable expression vector and a host cell, allowfor the convenient positive identification of polypeptides encoded bycloned DNAs, as well as for the rapid screening of such polypeptides fordesired properties.

(ix) Suitable Exemplary Vertebrate Cell Vectors

Other methods, vectors, and host cells suitable for adaptation to thesynthesis of vSmo in recombinant vertebrate cell culture are describedin Gething et al., Nature, 293:620-625 (1981); Mantei et al., Nature,281:40-46 (1979); EP 117,060; and EP 117,058.

3. Selection and Transformation of Host Cells

Suitable host cells for cloning or expressing the DNA in the vectorsherein are the prokaryote, yeast, or higher eukaryote cells describedabove. Suitable prokaryotes for this purpose include but are not limitedto eubacteria, such as Gram-negative or Gram-positive organisms, forexample, Enterobacteriaceae such as Escherichia. Preferably, the hostcell should secrete minimal amounts of proteolytic enzymes.

In addition to prokaryotes, eukaryotic microbes such as filamentousfungi or yeast may be suitable cloning or expression hosts forvSmo-encoding vectors. Saccharomyces cerevisiae, or common baker'syeast, is the most commonly used among lower eukaryotic hostmicroorganisms. However, a number of other genera, species, and strainsare commonly available and useful herein.

Suitable host cells for the expression of glycosylated vSmo are derivedfrom multicellular organisms. Such host cells are capable of complexprocessing and glycosylation activities. In principle, any highereukaryotic cell culture is workable, whether from vertebrate orinvertebrate culture. Examples of invertebrate cells include plant andinsect cells.

Propagation of vertebrate cells in culture (tissue culture) is also wellknown in the art [See, e.g., Tissue Culture, Academic Press, Kruse andPatterson, editors (1973)]. Examples of useful mammalian host cell linesare monkey kidney CV1 line transformed by SV40 (COS-7, ATCC CRL 1651);human embryonic kidney line (293 or 293 cells subcloned for growth insuspension culture, Graham et al., J. Gen Virol., 36:59 (1977)); babyhamster kidney cells (BHK, ATCC CCL 10); Chinese hamster ovarycells/-DHFR (CHO, Urlaub and Chasin, Proc. Natl. Acad. Sci. USA, 77:4216(1980)); mouse sertoli cells (TM4, Mather, Biol. Reprod., 23:243-251(1980)); monkey kidney cells (CV1 ATCC CCL 70); African green monkeykidney cells (VERO-76, ATCC CRL-1587); human cervical carcinoma cells(HELA, ATCC CCL 2); canine kidney cells (MDCK, ATCC CCL 34); buffalo ratliver cells (BRL 3A, ATCC CRL 1442); human lung cells (W138, ATCC CCL75); human liver cells (Hep G2, HB 8065); mouse mammary tumor (MMT060562, ATCC CCL51); TRI cells (Mather et al., Annals N.Y. Acad. Sci.,383:44-68 (1982)); MRC 5 cells; and FS4 cells.

Host cells are transfected and preferably transformed with theabove-described expression or cloning vectors for vSmo production andcultured in conventional nutrient media modified as appropriate forinducing promoters, selecting transformants, or amplifying the genesencoding the desired sequences.

Transfection refers to the taking up of an expression vector by a hostcell whether or not any coding sequences are in fact expressed. Numerousmethods of transfection are known to the ordinarily skilled artisan, forexample, CaPO₄ and electroporation. Successful transfection is generallyrecognized when any indication of the operation of this vector occurswithin the host cell.

Transformation means introducing DNA into an organism so that the DNA isreplicable, either as an extrachromosomal element or by chromosomalintegrant. Depending on the host cell used, transformation is done usingstandard techniques appropriate to such cells. The calcium treatmentemploying calcium chloride, as described in Sambrook et al., supra, orelectroporation is generally used for prokaryotes or other cells thatcontain substantial cell-wall barriers. Infection with Agrobacteriumtumefaciens is used for transformation of certain plant cells, asdescribed by Shaw et al., Gene, 23:315 (1983) and WO 89/05859 publishedJun. 29, 1989. In addition, plants may be transfected using ultrasoundtreatment as described in WO 91/00358 published Jan. 10, 1991.

For mammalian cells without such cell walls, the calcium phosphateprecipitatn method of Graham and van der Eb, Virology, 52:456-457 (1973)is preferred. General aspects of mammalian cell host systemtransformations have been described in U.S. Pat. No. 4,399,216.Transformations into yeast are typically carried out according to themethod of Van Solingen et al., J. Bact., 130:946 (1977) and Hsiao etal., Proc. Natl. Acad. Sci. (USA), 76:3829 (1979). However, othermethods for introducing DNA into cells, such as by nuclearmicroinjection, electroporation, bacterial protoplast fusion with intactcells, or polycations, e.g., polybrene, polyornithine, may also be used.For various techniques for transforming mammalian cells, see Keown etal., Methods in Enzymology, 185:527-537 (1990) and Mansour et al.,Nature, 336:348-352 (1988).

4. Culturing the Host Cells

Prokaryotic cells used to produce vSmo may be cultured in suitable mediaas described generally in Sambrook et al., supra.

The mammalian host cells used to produce vSmo may be cultured in avariety of media. Examples of commercially available media include Ham'sF10 (Sigma), Minimal Essential Medium (“MEM”, Sigma), RPMI-1640 (Sigma),and Dulbecco's Modified Eagle's Medium (“DMEM”, Sigma). Any such mediamay be supplemented as necessary with hormones and/or other growthfactors (such as insulin, transferrin, or epidermal growth factor),salts (such as sodium chloride, calcium, magnesium, and phosphate),buffers (such as HEPES), nucleosides (such as adenosine and thymidine),antibiotics (such as Gentamycin™ drug), trace elements (defined asinorganic compounds usually present at final concentrations in themicromolar range), and glucose or an equivalent energy source. Any othernecessary supplements may also be included at appropriate concentrationsthat would be known to those skilled in the art. The culture conditions,such as temperature, pH, and the like, are those previously used withthe host cell selected for expression, and will be apparent to theordinarily skilled artisan.

In general, principles, protocols, and practical techniques formaximizing the productivity of mammalian cell cultures can be found inMammalian Cell Biotechnology: a Practical Approach, M. Butler, ed. (IRLPress, 1991).

The host cells referred to in this disclosure encompass cells in cultureas well as cells that are within a host animal.

5. Detecting Gene Amplification/Expression

Gene amplification and/or expression may be measured in a sampledirectly, for example, by conventional Southern blotting, Northernblotting to quantitate the transcription of mRNA [Thomas, Proc. Natl.Acad. Sci. USA, 77:5201-5205 (1980)], dot blotting (DNA analysis), or insitu hybridization, using an appropriately labeled probe, based on thesequences provided herein. Various labels may be employed, most commonlyradioisotopes, and particularly ³²P, However, other techniques may alsobe employed, such as using biotin-modified nucleotides for introductioninto a polynucleotide. The biotin then serves as the site for binding toavidin or antibodies, which may be labeled with a wide variety oflabels, such as radionucleotides, fluorescers or enzymes. Alternatively,antibodies may be employed that can recognize specific duplexes,including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes orDNA-protein duplexes. The antibodies in turn may be labeled and theassay may be carried out where the duplex is bound to a surface, so thatupon the formation of duplex on the surface, the presence of antibodybound to the duplex can be detected.

Gene expression, alternatively, may be measured by immunologicalmethods, such as immunohistochemical staining of cells or tissuesections and assay of cell culture or body fluids, to quantitatedirectly the expression of gene product. With immunohistochemicalstaining techniques, a cell sample is prepared, typically by dehydrationand fixation, followed by reaction with labeled antibodies specific forthe gene product coupled, where the labels are usually visuallydetectable, such as enzymatic labels, fluorescent labels, or luminescentlabels.

Antibodies useful for immunohistochemical staining and/or assay ofsample fluids may be either monoclonal or polyclonal, and may beprepared in any mammal. Conveniently, the antibodies may be preparedagainst a native sequence vSmo protein or against a synthetic peptidebased on the DNA sequences provided herein.

6. Purification of vSmo

It is contemplated that it may be desired to purify some form of vSmofrom recombinant cell proteins or polypeptides to obtain preparationsthat are substantially homogeneous to vSmo. As a first step, the culturemedium or lysate may be centrifuged to remove particulate cell debris.vSmo thereafter may be purified from contaminant soluble proteins andpolypeptides, with the following procedures being exemplary of suitablepurification procedures: by fractionation on an ion-exchange column;ethanol precipitation; reverse phase HPLC; chromatography on silica oron a cation-exchange resin such as DEAE; chromatofocusing; SDS-PAGE;ammonium sulfate precipitation; gel filtration using, for example,Sephadex G-75; and protein A Sepharose columns to remove contaminantssuch as IgG. vSmo variants may be recovered in the same fashion asnative sequence vSmo, taking account of any substantial changes inproperties occasioned by the variation.

A protease inhibitor such as phenyl methyl sulfonyl fluoride (PMSF) alsomay be useful to inhibit proteolytic degradation during purification,and antibiotics may be included to prevent the growth of adventitiouscontaminants.

7. Covalent Modifications of vSmo

Covalent modifications of vSmo are included within the scope of thisinvention. One type of covalent modification of the vSmo included withinthe scope of this invention comprises altering the native glycosylationpattern of the protein. “Altering the native glycosylation pattern” isintended for purposes herein to mean deleting one or more carbohydratemoieties found in native sequence vSmo, and/or adding one or moreglycosylation sites that are not present in the native sequence vSmo.

Glycosylation of polypeptides is typically either N-linked or O-linked.N-linked refers to the attachment of the carbohydrate moiety to the sidechain of an asparagine residue. The tripeptide sequencesasparagine-X-serine and asparagine-X-threonine, where X is any aminoacid except proline, are the recognition sequences for enzymaticattachment of the carbohydrate moiety to the asparagine side chain.Thus, the presence of either of these tripeptide sequences in apolypeptide creates a potential glycosylation site. O-linkedglycosylation refers to the attachment of one of the sugarsN-aceylgalactosamine, galactose, or xylose to a hydroxylamino acid, mostcommonly serine or threonine, although 5-hydroxyproline or5-hydroxylysine may also be used.

Addition of glycosylation sites to the vSmo may be accomplished byaltering the amino acid sequence such that it contains one or more ofthe above-described tripeptide sequences (for N-linked glycosylationsites). The alteration may also be made by the addition of, orsubstitution by, one or more serine or threonine residues to the nativesequence vSmo (for O-linked glycosylation sites). The vSmo amino acidsequence may optionally be altered through changes at the DNA level,particularly by mutating the DNA encoding the vSmo protein atpreselected bases such that codons are generated that will translateinto the desired amino acids. The DNA mutation(s) may be made usingmethods described above and in U.S. Pat. No. 5,364,934, supra.

Another means of increasing the number of carbohydrate moieties on thevSmo is by chemical or enzymatic coupling of glycosides to thepolypeptide. Depending on the coupling mode used, the sugar(s) may beattached to (a) arginine and histidine, (b) free carboxyl groups, (c)free sulfhydryl groups such as those of cysteine, (d) free hydroxylgroups such as those of serine, threonine, or hydroxyproline, (e)aromatic residues such as those of phenylalanine, tyrosine, ortryptophan, or (f) the amide group of glutamine. These methods aredescribed in WO 87/05330 published Sep. 11, 1987, and in Aplin andWriston, CRC Crit. Rev. Biochem., pp. 259-306 (1981).

Removal of carbohydrate moieties present on the vSmo protein may beaccomplished chemically or enzymatically or by mutational substitutionof codons encoding for amino acid residues that serve as targets forglycosylation. For instance, chemical deglycosylation by exposing thepolypeptide to the compound trifluoromethanesulfonic acid, or anequivalent compound can result in the cleavage of most or all sugarsexcept the linking sugar (N-acetylglucosamine or N-acetylgalactosamine),while leaving the polypeptide intact. Chemical deglycosylation isdescribed by Hakimuddin, et al., Arch. Biochem. Biophys., 259:52 (1987)and by Edge et al., Anal. Biochem., 118:131 (1981). Enzymatic cleavageof carbohydrate moieties on polypeptides can be achieved by the use of avariety of endo- and exo-glycosidases as described by Thotakura et al.,Meth. Enzymol., 138:350 (1987).

Glycosylation at potential lycosylation sites may be prevented by theuse of the compound tunicamycin as described by Duksin el al., J. Biol.Chem., 257:3105 (1982). Tunicamycin blocks the formation ofprotein-N-(lycoside linkages.

8. vSmo Chimeras

The present invention also provides chimeric molecules comprising vSmofused to another, heterologous amino acid sequence or polypeptide. Inone embodiment, the chimeric molecule comprises a fusion of the vSmowith a tag polypeptide which provides an epitope to which an anti-tagantibody can selectively bind. The epitope tag is generally provided atthe amino- or carboxyl-terminus of the vSmo. Such epitope-tagged formsof the vSmo are desirable as the presence thereof can be detected usinga labeled antibody against the tag polypeptide. Also, provision of theepitope tag enables the vSmo to be readily purified by affinitypurification using the anti-tag antibody. Affinity purificationtechniques and diagnostic assays involving antibodies are describedlater herein.

Tag polypeptides and their respective antibodies are well known in theart. Examples include the flu HA tag polypeptide and its antibody 12CA5[Field et al., Mol. Cell. Biol., 8:2159-2165 (1988)]; the c-myc tag andthe 8F9, 3C7, 6E10, G4, B7 and 9E10 antibodies thereto [Evan et al.,Molecular and Cellular Biology, 5:3610-3616 (1985)]; and the HerpesSimplex virus glycoprotein D (gD) tag and its antibody [Paborsky el al.,Protein Engineering, 3(6):547-553 (1990)]. Other tag polypeptides havebeen disclosed. Examples include the Flag-peptide [Hopp el al.,BioTechnology, 6:1204-1210 (1988)]; the KT3 epitope peptide [Martin etal., Science, 255:192-194 (1992)]; an α-tubulin epitope peptide [Skinneret al., J. Biol. Chem., 266:14163-14166 (1991)]; and the T7 gene 10protein peptide tag [Lutz-Freyermuth et al., Proc. Natl. Acad. Sci. USA,87:6393-6397 (1990)]. Once the tag polypeptide has been selected, anantibody thereto can be generated using the techniques disclosed herein.

The general methods suitable for the construction and production ofepitope-tagged vSmo are the same as those disclosed hereinabove.vSmo-tag polypeptide fusions are most conveniently constructed by fusingthe cDNA sequence encoding the vSmo portion in-frame to the tagpolypeptide DNA sequence and expressing the resultant DNA fusionconstruct in appropriate host cells. Ordinarily, when preparing thevSmo-tag polypeptide chimeras of the present invention, nucleic acidencoding the vSmo will be fused at its 3′ end to nucleic acid encodingthe N-terminus of the tag polypeptide, however 5′ fusions are alsopossible.

9. Methods of Using vSmo

vSmo, as disclosed in the present specification, has utility intherapeutic and non-therapeutic applications. As a therapeutic, vSmo (orthe nucleic acid encoding the same) can be employed in in vivo or exvivo gene therapy techniques. In non-therapeutic applications, nucleicacid sequences encoding the vSmo may be used as a diagnostic fortissue-specific typing. For example, procedures like in situhybridization, Northern and Southern blotting, and PCR analysis may beused to determine whether DNA and/or RNA encoding vSmo is present in thecell type(s) being evaluated. vSmo nucleic acid will also be useful forthe preparation of vSmo by the recombinant techniques described herein.

The isolated vSmo may be used in quantitative diagnostic assays as acontrol against which samples containing unknown quantities of vSmo maybe prepared. vSmo preparations are also useful in generating antibodies,as standards in assays for vSmo (e.g., by labeling vSmo for use as astandard in a radioimmunoassay, radioreceptor assay, or enzyme-linkedimmunoassay), and in affinity purification techniques.

Nucleic acids which encode vSmo, such as the rat vSmo disclosed herein,can also be used to generate either transgenic animals or “knock out”animals which, in turn, are useful in the development and screening oftherapeutically useful reagents. A transgenic animal (e.g., a mouse orrat) is an animal having cells that contain a transgene, which transgenewas introduced into the animal or an ancestor of the animal at aprenatal, e.g., an embryonic stage. A transgene is a DNA which isintegrated into the genome of a cell from which a transgenic animaldevelops. In one embodiment, rat cDNA encoding rSmo or an appropriatesequence thereof can be used to clone genomic DNA encoding Smo inaccordance with established techniques and the genomic sequences used togenerate transgenic animals that contain cells which express DNAencoding Smo. Methods for generating transgenic animals, particularlyanimals such as mice or rats, have become conventional in the art andare described, for example, in U.S. Pat. Nos. 4,736,866 and 4,870,009.Typically, particular cells would be targeted for vSmo transgeneincorporation with tissue-specific enhancers. Transgenic animals thatinclude a copy of a transgene encoding vSmo introduced into the germline of the animal at an embryonic stage can be used to examine theeffect of increased expression of DNA encoding vSmo. Such animals can beused as tester animals for reagents thought to confer protection from,for example, pathological conditions associated with constitutiveactivity of vSmo or Hedgehog, including some forms of cancer that mayresult therefrom, such as for example, basal cell carcinoma, basal cellnevus syndrome and pancreatic carcinoma. In accordance with this facetof the invention, an animal is treated with the reagent and a reducedincidence of the pathological condition, compared to untreated animalsbearing the transgene, would indicate a potential therapeuticintervention for the pathological condition.

Alternatively, the non-human homologues of vSmo can be used to constructa vSmo “knock out” animal which has a defective or altered gene encodingvSmo as a result of homologous recombination between the endogenous geneencoding vSmo and altered genomic DNA encoding vSmo introduced into anembryonic cell of the animal. For example, rat cDNA encoding Smo can beused to clone genomic DNA encoding Smo in accordance with establishedtechniques. A portion of the genomic DNA encoding Smo can be deleted orreplaced with another gene. such as a gene encoding a selectable markerwhich can be used to monitor integration. Typically, several kilobasesof unaltered flanking DNA (both at the 5′ and 3′ ends) are included inthe vector [see e.g., Thomas and Capecchi, Cell, 51:503 (1987) for adescription of homologous recombination vectors]. The vector isintroduced into an embryonic stem cell line (e.g., by electroporation)and cells in which the introduced DNA has homologously recombined withthe endogenous DNA are selected [see e.g., Li et al., Cell, 69:915(1992)]. The selected cells are then injected into a blastocyst of ananimal (e.g, a mouse or rat) to form aggregation chimeras [see e.g.,Bradley, in Teratocarcinomas and Embryonic Stem Cells: A PracticalApproach, E. J. Robertson, ed. (IRL, Oxford, 1987), pp. 113-151]. Achimeric embryo can then be implanted into a suitable pseudopregnantfemale foster animal and the embryo brought to term to create a “knockout” animal. Progeny harboring the homologously recombined DNA in theirgerm cells can be identified by standard techniques and used to breedanimals in which all cells of the animal contain the homologouslyrecombined DNA. Knockout animals can be characterized for instance, fortheir ability to defend against certain pathological conditions and canbe used in the study of the mechanism by which the Hedgehog family ofmolecules exerts mitogenic, differentiative, and morphogenic effects.

B. Anti-vSmo Antibody Preparation

The present invention further provides anti-vSmo antibodies. Antibodiesagainst vSmo may be prepared as follows. Exemplary antibodies includepolyclonal, monoclonal, humanized, bispecific, and heteroconjugateantibodies.

1. Polyclonal Antibodies

The vSmo antibodies may comprise polyclonal antibodies. Methods ofpreparing polyclonal antibodies are known to the skilled artisan.Polyclonal antibodies can be raised in a mammal, for example, by one ormore injections of an immunizing agent and, if desired, an adjuvant.Typically, the immunizing agent and/or adjuvant will be injected in themammal by multiple subcutaneous or intraperitoneal injections. Theimmunizing agent may include the vSmo protein or a fusion proteinthereof. It may be useful to conjugate the immunizing agent to a proteinknown to be immunogenic in the mammal being immunized. Examples of suchimmunogenic proteins which may be employed include but are not limitedto keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, andsoybean trypsin inhibitor. An aggregating agent such as alum may also beemployed to enhance the mammal's immune response. Examples of adjuvantswhich may be employed include Freund's complete adjuvant and MPL-TDMadjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate).The immunization protocol may be selected by one skilled in the artwithout undue experimentation. The mammal can then be bled, and theserum assayed for antibody titer. If desired, the mammal can be boosteduntil the antibody titer increases or plateaus.

2. Monoclonal Antibodies

The vSmo antibodies may, alternatively, be monoclonal antibodies.Monoclonal antibodies may be prepared using hybridoma methods, such asthose described by Kohler and Milstein, supra. In a hybridoma method, amouse, hamster, or other appropriate host animal, is typically immunized(such as described above) with an immunizing agent to elicit lymphocytesthat produce or are capable of producing antibodies that willspecifically bind to the immunizing agent. Alternatively, thelymphocytes may be immunized in vitro.

The immunizing agent will typically include the vSmo protein or a fusionprotein thereof. Cells expressing vSmo at their surface may also beemployed. Generally, either peripheral blood lymphocytes (“PBLs”) areused if cells of human origin are desired, or spleen cells or lymph nodecells are used if non-human mammalian sources are desired. Thelymphocytes are then fused with an immortalized cell line using asuitable fusing agent, such as polyethylene glycol, to form a hybridomacell [Goding, Monoclonal Antibodies: Principles and Practice, AcademicPress, (1986) pp. 59-103]. Immortalized cell lines are usuallytransformed mammalian cells, particularly myeloma cells of rodent,bovine and human origin. Usually, rat or mouse myeloma cell lines areemployed. The hybridoma cells may be cultured in a suitable culturemedium that preferably contains one or more substances that inhibit thegrowth or survival of the unfused, immortalized cells. For example, ifthe parental cells lack the enzyme hypoxanthine guanine a phosphoribosyltransferase (HGPRT or HPRT), the culture medium for the hybridomastypically will include hypoxanthine, aminopterin, and thymidine (“HATmedium”), which substances prevent the growth of HGPRT-deficient cells.

Preferred immortalized cell lines are those that fuse efficiently,support stable high level expression of antibody by the selectedantibody-producing cells, and are sensitive to a medium such as HATmedium. More preferred immortalized cell lines are murine myeloma lines,which can be obtained, for instance, from the Salk Institute CellDistribution Center, San Diego, Calif. and the American Type CultureCollection, Rockville, Md. Human myeloma and mouse-human heteromyelomacell lines also have been described for the production of humanmonoclonal antibodies [Kozbor, J. Immunol., 133:3001 (1984); Brodeur etal., Monoclonal Antibody Production Techniques and Applications, MarcelDekker, Inc., New York, (1987) pp. 51-63].

The culture medium in which the hybridoma cells are cultured can then beassayed for the presence of monoclonal antibodies directed against vSmo.Preferably, the binding specificity of monoclonal antibodies produced bythe hybridoma cells is determined by immunoprecipitation or by an invitro binding assay, such as radioimmunoassay (RIA) or enzyme-linkedimmunosorbent assay (ELISA). Such techniques and assays are known in theart. The binding affinity of the monoclonal antibody can, for example,be determined by the Scatchard analysis of Munson and Pollard. Anal.Biochem., 107:220 (1980).

After the desired hybridoma cells are identified, the clones may besubcloned by limiting dilution procedures and grown by standard methods[Goding, supra]. Suitable culture media for this purpose include, forexample, Dulbecco's Modified Eagle's Medium and RPMI-1640 medium.Alternatively, the hybridoma cells may be grown in vivo as ascites in amammal.

The monoclonal antibodies secreted by the subclones may be isolated orpurified from the culture medium or ascites fluid by conventionalimmunoglobulin purification procedures such as, for example, proteinA-Sepharose, hydroxylapatite chromatography, gel electrophoresis,dialysis, or affinity chromatography.

The monoclonal antibodies may also be made by recombinant DNA methods,such as those described in U.S. Pat. No. 4,816,567. DNA encoding themonoclonal antibodies of the invention can be readily isolated andsequenced using conventional procedures (e.g., by using oligonucleotideprobes that are capable of binding specifically to genes encoding theheavy and light chains of murine antibodies). The hybridoma cells of theinvention serve as a preferred source of such DNA. Once isolated, theDNA may be placed into expression vectors, which are then transfectedinto host cells such as simian COS cells, Chinese hamster ovary (CHO)cells, or myeloma cells that do not otherwise produce immunoglobulinprotein, to obtain the synthesis of monoclonal antibodies in therecombinant host cells. The DNA also may be modified, for example, bysubstituting the coding sequence for human heavy and light chainconstant domains in place of the homologous murine sequences [U.S. Pat.No. 4,816,567; Morrison et al., supra] or by covalently joining to theimmunoglobulin coding sequence all or part of the coding sequence for anon-immunoglobulin polypeptide. Such a non-immunoglobulin polypeptidecan be substituted for the constant domains of an antibody of theinvention, or can be substituted for the variable domains of oneantigen-combining site of an antibody of the invention to create achimeric bivalent antibody.

The antibodies may be monovalent antibodies. Methods for preparingmonovalent antibodies are well known in the art. For example, one methodinvolves recombinant expression of immunoglobulin light chain andmodified heavy chain. The heavy chain is truncated generally at anypoint in the Fc region so as to prevent heavy chain crosslinking.Alternatively, the relevant cysteine residues are substituted withanother amino acid residue or are deleted so as to prevent crosslinking.

In vitro methods are also suitable for preparing monovalent antibodies.Digestion of antibodies to produce fragments thereof, particularly, Fabfragments, can be accomplished using routine techniques known in theart. For instance, digestion can be performed using papain. Examples ofpapain digestion are described in WO 94/29348 published Dec. 22, 1994and U.S. Pat. No. 4,342,566. Papain digestion of antibodies typicallyproduces two identical antigen binding fragments, called Fab fragments,each with a single antigen binding site, and a residual Fc fragment.Pepsin treatment yields an F(ab′)₂ fragment that has two antigencombining sites and is still capable of cross-linking antigen.

The Fab fragments produced in the antibody digestion also contain theconstant domains of the light chain and the first constant domain (CH₁)of the heavy chain. Fab′ fragments differ from Fab fragments by theaddition of a few residues at the carboxy terminus of the heavy chainCH₂ domain including one or more cysteines from the antibody hingeregion. Fab′-SH is the designation herein for Fab′ in which the cysteineresidue(s) of the constant domains bear a free thiol group. F(ab′)₂antibody fragments originally were produced as pairs of Fab′ fragmentswhich have hinge cysteines between them. Other chemical couplings ofantibody fragments are also known.

3. Humanized Antibodies

The vSmo antibodies of the invention may further comprise humanizedantibodies or human antibodies. Humanized forms of non-human (e.g.,murine) antibodies are chimeric immunoglobulins, immunoglobulin chainsor fragments thereof (such as Fv, Fab, Fab′, F(ab′)₂ or otherantigen-binding subsequences of antibodies) which contain minimalsequence derived from non-human immunoglobulin. Humanized antibodiesinclude human immunoglobulins (recipient antibody) in which residuesfrom a complementary determining region (CDR) of the recipient arereplaced by residues from a CDR of a non-human species (donor antibody)such as mouse, rat or rabbit having the desired specificity, affinityand capacity. In some instances, Fv framework residues of the humanimmunoglobulin are replaced by corresponding non-human residues.Humanized antibodies may also comprise residues which are found neitherin the recipient antibody nor in the imported CDR or frameworksequences. In general, the humanized antibody will comprisesubstantially all of at least one, and typically two, variable domains,in which all or substantially all of the CDR regions correspond to thoseof a non-human immunoglobulin and all or substantially all of the FRregions are those of a human immunoglobulin consensus sequence. Thehumanized antibody optimally also will comprise at least a portion of animmunoglobulin constant region (Fc), typically that of a humanimmunoglobulin [Jones et al., Nature, 321:522-525 (1986); Riechmann etal., Nature, 332:323-327 (1988); and Presta, Curr. Op. Struct. Biol.,2:593-596 (1992)].

Methods for humanizing non-human antibodies are well known in the art.Generally, a humanized antibody has one or more amino acid residuesintroduced into it from a source which is non-human. These non-humanamino acid residues are often referred to as “import” residues, whichare typically taken from an “import” variable domain. Humanization canbe essentially performed following the method of Winter and co-workers[Jones et al., Nature, 321:522-525 (1986); Riechmann et al., Nature,332:323-327 (1988); Verhoeyen et al., Science, 239:1534-1536 (1988)], bysubstituting rodent CDRs or CDR sequences for the correspondingsequences of a human antibody. Accordingly, such “humanized” antibodiesare chimeric antibodies (U.S. Pat. No. 4,816,567), wherein substantiallyless than an intact human variable domain has been substituted by thecorresponding sequence from a non-human species. In practice, humanizedantibodies are typically human antibodies in which some CDR residues andpossibly some FR residues are substituted by residues from analogoussites in rodent antibodies.

The choice of human variable domains, both light and heavy, to be usedin making the humanized antibodies is very important in order to reduceantigenicity. According to the “best-fit” method, the sequence of thevariable domain of a rodent antibody is screened against the entirelibrary of known human variable domain sequences. The human sequencewhich is closest to that of the rodent is then accepted as the humanframework (FR) for the humanized antibody [Sims et al., J. Immunol.,151:2296 (1993); Chothia and Lesk, J. Mol. Biol., 196:901 (1987)].Another method uses a particular framework derived from the consensussequence of all human antibodies of a particular subgroup of light orheavy chains. The same framework may be used for several differenthumanized antibodies [Carter et al., Proc. Natl. Acad. Sci. USA, 89:4285(1992); Presta et al., J. Immunol., 151:2623 (1993)].

It is further important that antibodies be humanized with retention ofhigh affinity for the antigen and other favorable biological properties.To achieve this goal, according to a preferred method, humanizedantibodies are prepared by a process of analysis of the parentalsequences and various conceptual humanized products using threedimensional models of the parental and humanized sequences. Threedimensional immunoglobulin models are commonly available and arefamiliar to those skilled in the art. Computer programs are availablewhich illustrate and display probable three-dimensional conformationalstructures of selected candidate immunoglobulin sequences. Inspection ofthese displays permits analysis of the likely role of the residues inthe functioning of the candidate immunoglobulin sequence, i.e., theanalysis of residues that influence the ability of the candidateimmunoglobulin to bind its antigen. In this way, FR residues can beselected and combined from the consensus and import sequence so that thedesired antibody characteristic, such as increased affinity for thetarget antigen(s), is achieved. In general, the CDR residues aredirectly and most substantially involved in influencing antigen binding[see, WO 94/04679 published Mar. 3, 1994].

Transgenic animals (e.g., mice) that are capable, upon immunization, ofproducing a full repertoire of human antibodies in the absence ofendogenous immunoglobulin production can be employed. For example, ithas been described that the homozygous deletion of the antibody heavychain joining region (J_(H)) gene in chimeric and germ-line mutant miceresults in complete inhibition of endogenous antibody production.Transfer of the human germ-line immunoglobulin gene array in suchgerm-line mutant mice will result in the production of human antibodiesupon antigen challenge [see, e.g., Jakobovits et al., Proc. Natl. Acad.Sci. USA, 90:2551-255 (1993); Jakobovits et al., Nature, 362:255-258(1993); Bruggemann et al., Year in Immuno., 7:33 (1993)]. Humanantibodies can also be produced in phage display libraries [Hoogenboomand Winter, J. Mol. Biol., 227:381 (1991); Marks et al., J. Mol. Biol.,222:581 (1991)]. The techniques of Cole et al. and Boerner et al. arealso available for the preparation of human monoclonal antibodies (Coleet al., Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, p. 77(1985) and Boerner et al., J. Immunol., 147(1):86-95 (1991)].

4. Bispecific Antibodies

Bispecific antibodies are monoclonal, preferably human or humanized,antibodies that have binding specificities for at least two differentantigens. In the present case, one of the binding specificities is forthe vSmo, the other one is for any other antigen, and preferably for acell-surface protein or receptor or receptor subunit.

Methods for making bispecitic antibodies are known in the art.Traditionally, the recombinant production of bispecific antibodies isbased on the co-expression of two immunoglobulin heavy-chain/light-chainpairs, where the two heavy chains have different specificities [Milsteinand Cuello. Nature, 305:537-539 (1983)]. Because of the randomassortment of immunoglobulin heavy and light chains, these hybridomas(quadromas) produce a potential mixture of ten different antibodymolecules, of which only one has the correct bispecific structure. Thepurification of the correct molecule is usually accomplished by affinitychromatography steps. Similar procedures are disclosed in WO 93/08829,published May 13, 1993, and in Traunecker el al., EMBO J., 10:3655-3659(1991).

According to a different and more preferred approach, antibody variabledomains with the desired binding specificities (antibody-antigencombining sites) are fused to immunoglobulin constant domain sequences.The fusion preferably is with an immunoglobulin heavy-chain constantdomain, comprising at least part of the hinge, CH2, and CH3 regions. Itis preferred to have the first heavy-chain constant region (CH1)containing the site necessary for light-chain binding present in atleast one of the fusions. DNAs encoding the immunoglobulin heavy-chainfusions and, if desired, the immunoglobulin light chain, are insertedinto separate expression vectors, and are co-transfected into a suitablehost organism. This provides for greatflexibility in adjusting themutual proportions of the three polypeptide fragments in embodimentswhen unequal ratios of the three polypeptide chains used in theconstruction provide the optimum yields. It is, however, possible toinsert the coding sequences for two or all three polypeptide chains inone expression vector when the expression of at least two polypeptidechains in equal ratios results in high yields or when the ratios are ofno particular significance. In a preferred embodiment of this approach,the bispecific antibodies are composed of a hybrid immunoglobulin heavychain with a first binding specificity in one arm, and a hybridimmunoglobulin heavy-chain/light-chain pair (providing a second bindingspecificity) in the other arm. It was found that this asymmetricstructure facilitates the separation of the desired bispecific compoundfrom unwanted immunoglobulin chain combinations, as the presence of animmunoglobulin light chain in only one half of the bispecific moleculeprovides for a facile way of separation. This approach is disclosed inWO 94/04690 published Mar. 3, 1994. For further details of generatingbispecific antibodies see, for example, Suresh et al., Methods inEnzymology, 121:210 (1986).

5. Heteroconjugate Antibodies

Heteroconjugate antibodies are also within the scope of the presentinvention. Heteroconjugate antibodies are composed of two covalentlyjoined antibodies. Such antibodies have, for example, been proposed totarget immune system cells to unwanted cells [U.S. Pat. No. 4,676,980],and for treatment of HIV infection [WO 91/00360; WO 92/20373; EP003089]. It is contemplated that the antibodies may be prepared in vitrousing known methods in synthetic protein chemistry, including thoseinvolving crosslinking agents. For example, immunotoxins may beconstructed using a disulfide exchange reaction or by forming athioether bond. Examples of suitable reagents for this purpose includeiminothiolate and methyl-4-mercaptobutyrimidate and those disclosed, forexample, in U.S. Pat. No. 4,676,980.

6. Uses of vSmo Antibodies

vSmo antibodies may be used in diagnostic assays for vSmo, e.g.,detecting its expression in specific cells or tissues. Variousdiagnostic assay techniques known in the art may be used, such ascompetitive binding assays, direct or indirect sandwich assays andimmunoprecipitation assays conducted in either heterogeneous orhomogeneous phases [Zola, Monoclonal Antibodies: A Manual of Techniques,CRC Press, Inc. (1987) pp. 147-158]. The antibodies used in thediagnostic assays can be labeled with a detectable moiety. Thedetectable moiety should be capable of producing, either directly orindirectly, a detectable signal. For example, the detectable moiety maybe a radioisotope, such as ³H, ¹⁴C, ³²P, ³⁵S, or ¹²⁵I, a fluorescent orchemiluminescent compound, such as fluorescein isothiocyanate,rhodamine, or luciferin, or an enzyme, such as alkaline phosphatase,beta-galactosidase or horseradish peroxidase. Any method known in theart for conjugating the antibody to the detectable moiety may beemployed, including those methods described by Hunter et al., Nature,144:945 (1962); David et al., Biochemistry, 13:1014 (1974); Pain et al.,J. Immunol. Meth., 40:219 (1981); and Nygren, J. Histochem. andCytochem., 30:407 (1982).

vSmo antibodies also are useful for the affinity detection orpurification of vSmo from recombinant cell culture or natural sources.In this process, the antibodies against vSmo are immobilized on asuitable support, such a Sephadex resin or filter paper, using methodswell known in the art. The immobilized antibody then is contacted with asample containing the vSmo, and thereafter the support is washed with asuitable solvent that will remove substantially all the material in thesample except the vSmo, which is bound to the immobilized antibody.Finally, the support is washed with another suitable solvent that willrelease the vSmo from the antibody.

The vSmo antibodies may also be employed as therapeutics. For example,vSmo antibodies may be used to block or neutralize excess vSmosignalling that may result from mutant or inactivated Patched.Accordingly, the vsmo antibodies may be used in the treatment of, oramelioration of symptoms caused by, a pathological condition resultingfrom or associated with excess vSmo or vSmo signalling. Optionally,agonistic vSmo antibodies can be employed to induce the formation of, orenhance or stimulate tissue regeneration, such as regeneration of skintissue, lung tissue, muscle (such as heart or skeletal muscle), neuraltissue (such as serotonergic neurons, motoneurons or straital neurons),bone tissue or gut tissue. This vSmo antibody therapy will be useful ininstances where the tissue has been damaged by disease, aging or trauma.

The vSmo antibodies may be used or administered to a patient in apharmaceutically-acceptable carrier. Suitable carriers and theirformulations are described in Remington's Pharmaceutical Sciences, 16thed., 1980, Mack Publishing Co., edited by Oslo et al. If the vSmoantibodies are to be administered to a patient, the antibodies can beadministered by injection (e.g., intravenous, intraperitoneal,subcutaneous, intramuscular), or by other methods such as infusion thatensure its delivery to the bloodstream in an effective form. Effectivedosages and schedules for administering the vSmo antibodies may bedetermined empirically, and making such determinations is within theskill in the art. Those skilled in the art will understand that thedosage of vSmo antibodies that must be administered will vary dependingon, for example, the patient which will receive the antibodies, theroute of administration, and other therapeutic agents being administeredto the mammal. Guidance in selecting appropriate doses for such vSmoantibodies is found in the literature on therapeutic uses of antibodies,e.g., Handbook of Monoclonal Antibodies, Ferrone et al., eds., NogesPublications, Park Ridge, N.J., (1985) ch. 22 and pp. 303-357; Smith etal., Antibodies in Human Diagnosis and Therapy, Haber et al., eds.,Raven Press, New York (1977) pp. 365-389. A typical daily dosage of thevSmo antibodies used alone might range from about 1 μg/kg to up to 100mg/kg of body weight or more per day, depending on the factors mentionedabove.

C. Kits Containing vSmo or vSmo Antibodies

In another embodiment of the invention, there are provided articles ofmanufacture and kits containing vSmo or vSmo antibodies. The article ofmanufacture typically comprises a container with a label. Suitablecontainers include, for example, bottles, vials, and test tubes. Thecontainers may be formed from a variety of materials such as glass orplastic. The container holds the vSmo or vSmo antibodies. The label onthe container may indicate directions for either in vivo or in vitrouse, such as those described above.

The kit of the invention will typically comprise the container describedabove and one or more other containers comprising materials desirablefrom a commercial and user standpoint, including buffers, diluents,filters, and package inserts with instructions for use.

D. Additional Compositions of Matter

In a further embodiment of the invention, there are provided proteincomplexes comprising vertebrate Smoothened protein. and vertebratePatched protein. As demonstrated in the Examples, vertebrate Smoothenedand vertebrate Patched can form a complex. The protein complex whichincludes vertebrate Smoothened and vertebrate Patched may also includevertebrate Hedgehog protein. Typically in such a complex, the vertebrateHedgehog binds to the vertebrate Patched but does not bind to thevertebrate Smoothened. In a preferred embodiment, the complex comprisingvertebrate Smoothened and vertebrate Patched is a receptor forvertebrate Hedgehog.

The invention also provides a vertebrate Patched which binds tovertebrate Smoothened. Optionally the vertebrate Patched comprises asequence which is a derivative of or fragment of a native sequencevertebrate Patched. The vertebrate Patched will typically consist of asequence which has less than 100% sequence identity with a nativesequence vertebrate Patched. In one embodiment, the vertebrate Patcheddirectly and specifically binds vertebrate Smoothened. Alternatively, itis contemplated that the vertebrate Patched may bind vertebrateSmoothened indirectly.

The following examples are offered for illustrative purposes only, andare not intended to limit the scope of the present invention in any way.

All references cited in the present specification are herebyincorporated by reference in their entirety.

EXAMPLES

All commercially available reagents referred to in the examples wereused according to manufacturer's instructions unless otherwiseindicated. The source of those cells identified in the followingexamples, and throughout the specification, by ATCC accession numbers isthe American Type Culture Collection. 10801 University Boulevard,Manassas, Va. 20110-2209.

Example 1

Isolation and Cloning of Rat Smoothened cDNA

Full-length rat Smoothened cDNA was isolated by low stringencyhybridization screening of 1.2×10⁶ plaques of an embryonic day 9-10 ratcDNA library (containing cDNAs size-selected>1500 base pairs), using theentire coding region of Drosophila Smoothened [Alcedo et. al., supra](labeled with ³²P-dCTP) as a probe. The library was prepared by cloningcDNA inserts into the NotI site of a lambda RK18 vector [Klein et. al.,Proc. Natl. Acad. Sci., 93:7108-7113 (1996)] following XmnI adaptersligation. Conditions for hybridization were: 5×SSC, 30% formamide,5×Denhardt's, 50 mM sodium phosphate (pH 6.5), 5% dextran sulfate, 0.1%SDS and 50 μg/ml salmon sperm DNA, overnight at 42° C. Nitrocellulosefilters were washed to a stringency of 1×SSC at 42° C., and exposedovernight to Kodak X-AR film. Three of eight positive plaques wereselected for further purification. After amplification of theplaque-purified phage, phagemid excision products were generated bygrowing M13 helper phage (M13K07; obtained from New England Biolabs),bacteria (BB4; obtained from Stratagene), and the purified phagetogether in a 100:10:1 ratio. Plasmid DNA was recovered by Qiagenpurification from ampicillin-resistant colonies following infection ofBB4 with the excised purified phagemid.

Sequencing of the three cDNAs showed them to be identical, with theexception that two contained only a partial coding sequence, whereas thethird contained the entire open reading frame of rat Smoothened,including 449 and 1022 nucleotides, respectively of 5′ and 3′untranslated sequence and a poly-A tail. This cDNA clone was sequencedcompletely on both strands.

The entire nucleotide sequence of rat Smoothened (rSmo) is shown in FIG.1 (SEQ ID NO:1) (reference is also made to Applicants' ATCC deposit ofthe rat Smoothened in pRK5.rsmo.AR140, assigned ATCC Dep. No. 98165).The cDNA contained an open reading frame with a translational initiationsite assigned to the ATG codon at nucleotide positions 450-452. The openreading frame ends at the termination codon at nucleotide positions2829-2831.

The predicted amino acid sequence of the rat Smoothened (rSmo) contains793 amino acids (including a 32 amino acid signal peptide), as shown inFIG. 1 (SEQ ID NO:2). rSmo appears to be a typical seven transmembrane(7 TM), G protein-coupled receptor, containing 4 potentialN-glycosylation sites and a 203 amino acid long putative extracellularamino-terminus domain which contains 13 stereotypically spaced cysteines(see FIG. 2).

An alignment of the rSmo sequence with sequences for dSmo, winglessreceptor and vertebrate Frizzled revealed that rSmo is 33% homologous tothe dSmo sequence reported in Alcedo et al., supra (50% homologous inthe transmembrane domains); 23% homologous to the wingless receptorsequence reported in Bhanot et al., supra; and 25% homologous to thevertebrate Frizzled sequence reported in Chan et al., supra.

Example 2

In Situ Hybridization and Northern Blot Analysis

In situ hybridization and Northern blot analyses were conducted toexamine tissue distribution of Smo, Patched and SHH in embryonic andadult rat tissues.

For in situ hybridization, E9-E15.5 rat embryos (Hollister Labs) wereimmersion-fixed overnight at 4° C. in 4% paraformaldehyde, thencryoprotected overnight in 20% sucrose. Adult rat brains and spinalcords were frozen fresh. All tissues were sectioned at 16 um, andprocessed for in situ hybridization using ³³P-UTP labelled RNA probes asdescribed in Treanor et al., Nature, 382:80-83 (1996). Sense andantisense probes were derived from the N-terminal region of rSmo usingT7 polymerase. The probe used to detect SHH was antisense to bases604-1314 of mouse SHH [Echelard et al., Cell, 75:1417-1430 (1993)]. Theprobe used to detect Patched was antisense to bases 502-1236 of mousePatched [Goodrich et al., supra]. Reverse transcriptase polymerase chainreaction analysis was performed as described in Treanor et al., supra.

The results are illustrated in FIG. 3. By in situ hybridization andNorthern blot analysis, expression of rSmo mRNA was detected from E9onward in SHh responsive tissues such as the neural folds and earlyneural tube [Echelard el al., supra, Krauss et al., supra); Roelink etal., supra]. pre-somitic mesoderm and somites (Johnson et al., supra;Fan et al., supra], and developing limb buds [Riddle et al., supra] gut(Roberts et al., supra] and eye [Krauss et al., spra]. Rat Smotranscripts were also found in tissues whose development is regulated byother members of the vertebrate Hh protein family such as testes (DesertHh) [Bitgood et al., Curr. Biol., 6:298-304 (1996)], cartilage (IndianHh) [Vortkamp et al., Science, 273:613-622 (1996)], and muscle (thezebra fish, echinida Hh) [Currie and Ingham, Nature, 382:452-455 (1996)](See e.g., FIG. 3; other data not shown). In all of the above recitedtissues, rSmo appeared to be co-expressed with rPatched.

rSmo and rPatched mRNAs were also found in and around SHH expressingcells in the embryonic lung, epiglottis, thymus, vertebral column,tongue, jaw, taste buds and teeth (FIG. 3). In the embryonic nervoussystem, rSmo and rPatched are initially expressed throughout the neuralplate; by E12, however, their expression declines in lateral parts ofthe neural tube, and by P1, was restricted to cells in relatively closeproximity to the ventricular zone (FIG. 3). In the adult rat tissues,rSmo expression was maintained in the brain, lung, kidney, testis, heartand spleen (data not shown).

Example 3

Isolation and Cloning of Human Smoothened cDNA

A cDNA probe corresponding to the coding region of the rat smoothenedgene (described in Example 1 above) was labeled by the randomhexanucleotide method and used to screen 10⁶ clones of a human embryoniclung cDNA library (Clontech, Inc.) in lgt10. Duplicate filters werehybridized at 42° C. in 50% formamide, 5×SSC, 10×Denhardt's, 0.05Msodium phosphate (pH 6.5), 0.1% sodium pyrophosphate, 50 μg/ml ofsonicated salmon sperm DNA. Filters were rinsed in 2×SSC and then washedonce in 0.5×SSC, 0.1% SDS at 42° C. Hybridizing phage wereplaque-purified and the cDNA inserts were subcloned into pUC 118 (NewEngland Biolabs). Two clones, 5 and 14, had overlapping inserts ofapproximately 2 and 2.8 kb respectively, covering the entire humanSmoothened coding sequence (See FIG. 4). Clones 5 and 14 have beendeposited by Applicants with ATCC as puc.118.hsmo.5 and puc.118.hsmo.14,respectively, and assigned ATCC Dep. Nos. 98162 and 98163, respectively.Both strands were sequenced by standard fluorescent methods on an ABI377automated sequencer.

The entire nucleotide sequence of human Smoothened is shown in FIG. 4(SEQ ID NO:3). The cDNA contained an open reading frame with atranslational initiation site assigned to the ATG codon at nucleotidepositions 13-15. The open reading frame ends at the termination codon atnucleotide positions 2374-2376.

The predicted amino acid sequence of the human Smoothened (hSmo)contains 787 amino acids (including a 29 amino acid signal peptide), asshown in FIG. 4 (SEQ ID NO:4). hSmo appears to be a typical seventransmembrane (7 TM), G protein-coupled receptor, containing 5 potentialN-glycosylation sites and a 202 amino acid long putative extracellularamino-terminus domain which contains 13 stereotypically spacedcysteines.

An alignment of the predicted hSmo amino acid sequence and rSmo sequence(see Example 1) revealed 94% amino acid identity.

An alignment of the hSmo sequence with sequences for dSmo, winglessreceptor and vertebrate Frizzled revealed that hSmo is 33% homologous tothe dSmo sequence reported in Alcedo et al., supra (50% homologous inthe transmembrane domains); 23% homologous to the wingless receptorsequence reported in Bhanot et al., supra; and 25% homologous to thevertebrate Frizzled sequence reported in Chan et al., supra. See FIG. 5for a comparison of theprimary sequences of human Smo, rat Smo andDrosophila Smo.

Example 4

Competitive Binding, Co-immunoprecipitation, and Cross-linking Assays

Competitive binding, co-immunoprecipitation and cross-linking assayswere conducted to characterize physical association or binding betweenSHH and rSmo, and between certain biologically active forms of SHH andcells expressing rSmo, mPatched, or both rSmo and mpatched.

1. Materials and Methods

Complementary DNAs for rSmo (described in Example 1); dSmo (described inAlcedo et al., supra); Desert HH (described in Echelard et al., supra);and murine Patched (described in Goodrich et al., supra) were clonedinto pRK5 vectors, and epitope tags [Flag epitope tag (Kodak/IBI) andMyc epitope tag (9E10 epitope; InVitrogen)] added to the extremeC-terminus by PCR-based mutagenesis.

SHH-N is the biologically active amino terminus portion of SHH [Lee etal., Science, 266:1528-1537 (1994)]. SHH-N was produced as described byHynes et al., supra. A radiolabeled form of SHH-N, ¹²⁵ISHH-N, wasemployed.

For IgG-SHH-N production, human embryonic kidney 293 cells weretransiently transfected with the expression vector encoding SHH-N fusedin frame after amino acid residue 198 to the Fc portion of humanIgG-gammal.

Cells were maintained in serum-free media (OptiMEM; Gibco BRL) for 48hours. The media was then collected and concentrated 10-fold using acentricon-10 membrane. Conditioned media was used at a concentration of2×.

Binding assays were conducted to test binding between cells expressingrSmo or dSmo and (1) epitope tagged SHH-N, (2) an IgG-SHH-N chimera, and(3) an epitope tagged Desert HH. For visualization of SHH binding, COS-7cells (Genentech, Inc.) transiently expressing rSmo or mPatched (murinePatched) were exposed to epitope tagged SHH-N (2 hours at 4° C.), washed4 times with PBS, then fixed and stained with a cy3-conjugatedanti-human IgG (Jackson ImmunoResearch) (for IgG-SHH-N) or anti-Flag M2antibody (Kodak/IBI) (for Flag-tagged SHH-N).

For immunohistochemistry, COS-7 cells transiently transfected withexpression constructs were fixed (10 minutes in 2% paraformaldehyde/0.2%Triton-X 100) and stained using monoclonal anti-Flag M2 antibody (IBI)or anti-Myc antibody (InVitrogen), followed by cy3-conjugated anti-mouseIgG (Jackson Immunoresearch)

For cross-linking, cells were resuspended at a density of 1-2×10⁶/ml inice-cold L15 media containing 0.1% BSA and 50 pM ¹²⁵I-labeled SHH (withor without a 1000-fold excess of unlabeled SHH) and incubated at 4° C.for 2 hr. 10 mM 1-ethyl-3-(3-dimethylaminopropyl)carbodimide carbodimideHCl and 5 mM N-hydroxysulfosuccinimide (Pierce Chemical) were added tothe samples and incubated at room temperature for 30 minutes. The cellswere then washed 3 times with 1 ml of PBS. Cells were then lysed inlysis buffer [1% Brij-96 (Sigma), 50 mM Tris, pH 8.0, 150 mM NaCl, 1 mMPMSF, 10 μM aprotinin, 10 μM leupeptin] and the protein complexes wereimmunoprecipitated with antibodies to the epitope tags as indicated.Immunoprecipitated proteins were resuspended in sample buffer (80 mMTris-HCl [pH 6.8], 10% [v/v] glycerol, 1% [w/v] SDS, 0.025% BromphenolBlue, denatured and run on 4% SDS-polyacrylamide gels, which were driedand exposed to film.

For the equilibrium binding analysis, the cells were processed as above,and incubated with 50 pM ¹²⁵I-SHH and various concentrations of coldSHH-N (Cold Ligand). The IGOR program was used to determine K_(d).

2. Results

The results are shown in FIG. 6. No binding of epitope tagged SHH-N, ofIgG-SHH-N chimeric protein or of an epitope tagged Desert HH to cellsexpressing rSmo or dSmo was observed (FIGS. 6a-b and data not shown).This data (and the data described below) indicated that rSmo, actingalone, would not likely be a receptor for SHH or Desert HH. However, itwas hypothesized that rSmo is a component in a multi-subunit SHHreceptor complex and that the ligand binding function of this receptorcomplex would be provided by another membrane protein such as Patched.

Binding assays were also conducted to test binding between cellsexpressing rSmo or murine patched and (1) an epitope tagged SHH and (2)an IgG-SHH-N chimera. The data shows that epitope tagged SHH-N as wellas an IgG-SHH-N chimeric protein bind specifically and reversibly tocells expressing the mouse Patched (mpatched) (mPatched is 33% identicalto Drosophila Patched) (FIGS. 6c-e). Furthermore, only mPatched could beimmunoprecipitated by the IgG-SHH-N protein (FIG. 6f) and antibodies toan epitope tagged mPatched readily co-immunoprecipitated ¹²⁵I-SHH-N(FIG. 6h) (antibodies to epitope tagged rSmo could not immunoprecipitate¹²⁵I-SHH-N and the IgG-SHH-N chimera did not immunoprecipitate rSmo).

As shown in FIG. 6g, the cross-linking assay of ¹²⁵I-SHH-N to cellsexpressing rSmo or mPatched in the presence or absence of cold SHH-Nrevealed that ¹²⁵I-SHH-N is cross-linked only to mPatched expressingcells.

The competitive binding assay of ¹²⁵I-SHH-N and cells expressingmPatched or mPatched plus rSmo also showed that mPatched and SHH-N had arelatively high affinity of interaction (approximate K_(d) of 460 pM)(FIG. 6i). This corresponds well to the concentrations of SHH-N whichare required to elicit biological responses in multiple systems [Fan etal., supra; Hynes et al. supra; Roelink et al., supra] . No binding tocells expressing rSmo alone was observed (data not shown) and there wasno increase in binding affinity to mPatched in the presence of rSmo.

Example 5

Co-immunoprecipitation Assays

To determine whether Patched and Smo form or interact in a physicalcomplex, co-immunoprecipitation experiments were performed.

1. Materials and Methods

For the double immunohistochemistry, COS-7 cells transiently transfectedwith expression constructs were permeabilized using 0.2% Triton-x 100.The cells were fixed (10 minutes in 2% paraformaldehyde/0.2% Triton-X100) and stained using monoclonal anti-Flag M2 antibody (IBI) and rabbitpolyclonal anti-Myc primary antibodies (Santa Cruz Biotech), followed bycy3-conjugated anti-mouse IgG (Jackson Immunoresearch) andbodipy-conjugated anti-rabbit IgG secondary antibodies (MolecularProbes, Inc.).

Human embryonic kidney 293 cells were transiently transfected withexpression vectors for epitope tagged rSmo (Flag epitope) and mPatched(Myc epitope) and the resulting proteins complexes wereimmunoprecipitated with antibody to one of the epitopes and thenanalyzed on a western blot.

For the co-immunoprecipitation assay, lysates from 293 embryonic kidneycells transiently expressing Flag-tagged rSmo, Myc-tagged mPatched or acombination of the two proteins were incubated (48 hours aftertransfection) in the presence or absence of the IgG-SHH-N chimera (1μg/ml, 30 minutes at 37° C.) or in the presence of ¹²⁵I-SHH-N with orwithout an excess of cold SHH-N (2 hours at 4° C.). The incubatedsamples were then washed 3 times with PBS, and lysed in lysis buffer(see Example 4) as described by Davis et al., Science, 259:1736-1739(1993). The cell lysates were centrifuged at 10,000 rpm for 10 minutes,and the soluble protein complexes were immunoprecipitated with eitherprotein A sepharose (for the IgG-SHH-N), or anti-Flag or anti-Mycantibodies followed by protein A sepharose (for the epitope-tagged rSmoor mPatched, respectively).

The samples were heated to 100° C. for 5 minutes in denaturing SDSsample buffer (125 mM Tris, pH 6.8, 2% SDS, 10% glycerol, 100 mMβ-mercaptoethanol, 0.05% bromphenol blue) and subjected to SDS-PAGE. Fheproteins were detected either by exposure of the dried gel to film (for¹²⁵I-SHH-N) or by blotting to nitrocellulose and probing with antibodiesto Flag or Myc epitopes using the ECL detection system (Amersham).

2. Results

The results are illustrated in FIG. 7. In cells expressing mPatchedalone, or rSmo alone, no co-immunoprecipitated protein complexes couldbe detected. In contrast, in cells that expressed both mPatched and rSmo(FIG. 7a), rSmo was readily co-immunoprecipitated by antibodies to theepitope tagged mPatched (FIG. 7b) and mPatched was co-immunoprecipitatedby antibodies to the epitope tagged rSmo (FIG. 7c).

The ¹²⁵I-SHH-N was readily co-immunoprecipitated by antibodies to theepitope tagged rSmo or mPatched from cells that expressed both rSmo andmpatched, but not from cells expressing rSmo alone (FIGS. 7d and 7 e).These results indicate that SHH-N, rSmo and mPatched are present in thesame physical complex, and that a rSmo-SHH complex does not form in theabsence of mpatched. Although not fully understood and not being boundby any particular theory, it is believed that Patched is a ligandbinding component and vSmo is a signalling component in a multi-subunitSHH receptor (See, FIG. 9). Patched is also believed to be a negativeregulator of vSmo.

Example 6

Hahn et al., supra, Johnson et al., supra, and Gailani et al., supra,report that Patched mutations have been associated with BCNS andsporadic basal cell carcinoma (“BCC”). These investigators also reportthat most of the Patched mutations in BCNS are truncations in which nofunctional protein is produced. It is believed that BCNS and BCC may becaused or associated with constitutive activation of vSmo, following itsrelease from negative regulation by Patched.

Expression levels of wild-type (native) murine Patched and a mutantPatched were examined. A Patched mutant was generated by site-directedmutagenesis of the wild-type mouse Patched cDNA (described in Example 4)and verified by sequencing. The mutant Patched contained a 3 amino acidinsertion (Pro-Asn-Ile) after amino acid residue 815 (this mutant wasfound in a BCNS family, see, Hahn et al., supra). For analysis ofprotein expression, equal amounts of pRK5 expression vectors containingwild-type or mutant Patched were transfected into 293 cells, and anequal number of cells (2×10⁶) were lysed per sample. Proteins wereimmunoprecipitated from cell lysates by antibody to the Patched epitopetag (myc) and detected on a Western blot with the same antibody.

Applicants found that expression of the mutant Patched (which retains acomplete open reading frame) was reduced at least 10-fold as compared toits wild-type counterpart. See FIG. 8.

DEPOSIT OF MATERIAL

The following materials have been deposited with the American TypeCulture Collection, 10801 University Boulevard, Manassas, Va. 20110-2209(ATCC):

Material ATCC Dep. No. Deposit Date puc.118.hsmo.5 98162 Sept. 6, 1996puc.118.hsmo.14 98163 Sept. 6, 1996 pRK5.rsmo.AR140 98165 Sept. 10, 1996

This deposit was made under the provisions of the Budapest Treaty on theInternational Recognition of the Deposit of Microorganisms for thePurpose of Patent Procedure and the Regulations thereunder (BudapestTreaty). This assures maintenance of a viable culture of the deposit for30 years from the date of deposit. The deposit will be made available byATCC under the terms of the Budapest Treaty, and subject to an agreementbetween Genentech, Inc. and ATCC, which assures permanent andunrestricted availability of the progeny of the culture of the depositto the public upon issuance of the pertinent U.S. patent or upon layingopen to the public of any U.S. or foreign patent application, whichevercomes first, and assures availability of the progeny to one determinedby the U.S. Commissioner of Patents and Trademarks to be entitledthereto according to 35 USC §122 and the Commissioner's rules pursuantthereto (including 37 CFR §1.14 with particular reference to 886 OG638).

The assignee of the present application has agreed that if a culture ofthe materials on deposit should die or be lost or destroyed whencultivated under suitable conditions, the materials will be promptlyreplaced on notification with another of the same. Availability of thedeposited material is not to be construed as a license to practice theinvention in contravention of the rights granted under the authority ofany government in accordance with its patent laws.

The foregoing written specification is considered to be sufficient toenable one skilled in the art to practice the invention. The presentinvention is not to be limited in scope by the construct deposited,since the deposited embodiment is intended as a single illustration ofcertain aspects of the invention and any constructs that arefunctionally equivalent are within the scope of this invention. Thedeposit of material herein does not constitute an admission that thewritten description herein contained is inadequate to enable thepractice of any aspect of the invention, including the best modethereof, nor is it to be construed as limiting the scope of the claimsto the specific illustrations that it represents. Indeed, variousmodifications of the invention in addition to those shown and describedherein will become apparent to those skilled in the art from theforegoing description and fall within the scope of the appended claims.

What is claimed is:
 1. An antibody which specifically binds to avertebrate Smoothened polypeptide, wherein said Smoothened polypeptide:(a) directly binds Patched; and (b) is encoded by a nucleic acid whichhybridizes to the complement of the nucleic acid sequence encodingresidues 1 to 787 of SEQ ID NO:4 under the following conditions:hybridization at 42° C. in 50% formamide, 5×SSC, 10×Denhardt's, 0.05Msodium phosphate (pH 6.5), 0.1% sodium pyrophosphate, 50 μg/ml sonicatedsalmon sperm; and rinsing with 2×SSC and washing with 0.5×SSC, 0.1% SDSat 42° C.
 2. The antibody of claim 1 which is a monoclonal antibody. 3.The antibody of claim 1 which is bispecific.
 4. The antibody of claim 1which is heteroconjugated.
 5. The antibody of claim 1 which is amonoclonal antibody fragment.
 6. The antibody frament of claim 5 whichis an Fab fragment.
 7. The antibody fragment of claim 5 which is anF(ab′)₂ fragment.
 8. The antibody fragment of claim 5 which is an Fvfragment.
 9. An article of manufacture, comprising a container enclosinga composition, wherein said composition comprises the anti-Smoothenedantibody of claim 1 and a pharmaceutically-acceptablc carer.
 10. Thearticle of manufacture of claim 9, further comprising instructions forusing said anti-Smoothened antibody in vivo or ex vivo.
 11. An antibodywhich specifically binds to a vertebrate Smoothened polypeptidc, whereinsaid Smoothened polypeptide: (a) directly binds Patched; and (b) isencoded by a nucleic acid which hybridizes to the complement of thenucleic acid sequence encoding residues 1 to 793 of SEQ ID NO:2 underthe following conditions: hybridization at 42° C. in 50% formamide,5×SSC, 10×Denhardt's, 0.05M sodium phosphate (pH 6.5), 0.1% sodiumpyrophosphate, 50 μg/ml sonicated salmon sperm; and rinsing with 2×SSCand washing with 0.5×SSC, 0.1% SDS at 42° C.
 12. The antibody of claim11 which is a monoclonal antibody.
 13. The antibody of claim 11 which isbispecific.
 14. The antibody of claim 11 which is heteroconjugated. 15.The antibody of claim 11 which is a monoclonal antibody fragment. 16.The antibody fragment of claim 15 which is an Fab fragment.
 17. Theantibody fragment of claim 15 which is an F(ab′)2 fragment.
 18. Theantibody fragment of claim 15 which is an Fv fragment.
 19. An antibodywhich specifically binds to an ECD of the Smoothened polypeptide of SEQID NO:4.
 20. The antibody of claim 19 which is a monoclonal antibody.21. The antibody of claim 19 which is bispecific.
 22. The antibody ofclaim 19 which is heteroconjugated.
 23. The antibody of claim 19 whichis an antibody fragment.
 24. The antibody fragment of claim 23 which isan Fab fragment.
 25. The antibody fragment of claim 23 which is anF(ab′)₂ fragment.
 26. The antibody fragment of claim 23 which is an Fvfragment.
 27. An article of manufacture, comprising a containerenclosing a composition, wherein said composition comprises theanti-Smoothened antibody of claim 19 and a pharmaceutically-acceptablecarrier.
 28. The article of manufacture of claim 27, further comprisinginstructions for using said anti-Smoothened antibody in vivo or ex vivo.29. An antibody which specifically binds to a vertebrate Smoothenedpolypeptide, wherein said vertebrate Smoothened polypeptide: (1)directly binds Patched and (2) is encoded by a nucleic acid whichhybridizes to the complement of the nucleic acid sequence of the humancDNA insert of ATCC Dep. No. 98162 under the following conditions:hybridization at 42° C. in 50% formamide, 5×SSC, 10×Denhardt's, 0.05Msodium phosphate (pH 6.5), 0.1% sodium pyrophosphate, 50 μg/ml sonicatedsalmon sperm; and rinsing with 2×SSC and washing with 0.5×SSC, 0.1% SDSat 42° C.
 30. An antibody which specifically binds to a vertebrateSmoothened polypeptide, wherein said vertebrate Smoothened polypeptide:(1) directly binds Patched and (2) is encoded by a nucleic acid whichhybridizes to the complement of the nucleic acid sequence of the humancDNA insert of ATCC Dep. No. 98163 under the following conditions:hybridization at 42° C. in 50% formamide, 5×SSC, 10×Denhardt's, 0.05Msodium phosphate (pH 6.5), 0.1% sodium pyrophosphate, 50 μg/ml sonicatedsalmon sperm; and rinsing with 2×SSC and washing with 0.5×SSC, 0.1% SDSat 42° C.
 31. An antibody which specifically binds to a vertebrateSmoothened polypeptide, wherein said vertebrate Smoothened polypeptide:(1) directly binds Patched and (2) is encoded by a nucleic acid whichhybridizes to the complement of the nucleic acid sequence of the humancDNA insert of ATCC Dep. No. 98165 under the following conditions:hybridization at 42° C. in 50% formamide, 5×SSC, 10×Denhardt's, 0.05Msodium phosphate (pH 6.5), 0.1% sodium pyrophosphate, 50 μg/ml sonicatedsalmon sperm; and rinsing with 2×SSC and washing with 0.5×SSC, 0.1% SDSat 42° C.